The paper has nothing to do with punctuated equilibrum vs. gradualism (see also here), which was published a few years earlier. This debate is much different (but equally important, I think).
The authors of the Spandrels paper criticized evolutionary biologists of taking a very narrow view of the evolutionary process. They claiming (wrongly) that evolutionary biologists believed that every single trait on an organism was an adaptation that resulted from natural selection. The trait would not be present unless it was an adaptation. The authors claimed (rightly) that traits could not be considered independently. Instead, the traits had to be considered in light of the evolutionary history and developmental biology of the organism. To your specific questions:
The architectural metaphor was wrong. Does it make their entire argument wrong? No. They did not understand architecture. That does not mean they did not understand evolutionary biology.
Are some of their claims wrong? I think yes and no, but the full answer requires more nuance than can really be given here so read the long answer below if interested. I don't know of a single reference that supports/rebuts the Spandrels paper but consider Why Evolution is True by Jerry Coyne, The Greatest Show in Earth by Richard Dawkins, and Endless Forms Most Beautiful by Sean Carroll. None of these address directly the charges lodged by the Spandrels paper but they do show how evolutionary biology is integrative of many ideas instead of isolating each trait without considering the biology of the entire organism. (I have no commerical interest in any of these books. I simply support the ideas presented.)
Long version from my perspective.
In 1979, Stephen J. Gould and Richard C. Lewontin (hereafter, G&L) published a paper, "The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme", in the Proceedings of the Royal Society of London, Series B. The title of the paper mixes two metaphors. The first is the character Dr. Pangloss from Voltaire's "Candide." Dr. Pangloss is a bit of an optimist, who says,
It is demonstrable ... that things cannot be otherwise than as they are; for as all things have been created for some end, they must necessarily be created for the best end. Observe, for instance, the nose is formed for spectacles, therefore we wear spectacles. The legs are visibly designed for stockings, accordingly we wear stockings. ... [A]nd they, who assert that everything is right, do not express themselves correctly; they should say that everything is best." - Dr. Pangloss
Dr. Pangloss is saying that everything has a purpose, and each thing is designed specifically for that purpose. G&L extend this metaphor to evolutionary biologists. G&L claim that evolutionary biologists (at least to the time of their publication) tended to make claims similar to Dr. Pangloss: every trait that could be found on an organism results from natural selection and adaptation. G&L write,
An adaptationist programme has dominated evolutionary thought in England and the United States during the past forty years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an organism into unitary "traits" and proposing an adaptive story for each considered separately. - G&L
Hence, the Panglossian paradigm. Every trait has an adaptive purpose and is necessarily the "best" that it can be. G&L then argue that evolutionary biologists of the time failed to consider the entire organism when assigning adaptive value to each trait separately.
We criticize this approach and attempt to reassert a competing notion ... that organisms must be analyzed as integrated wholes, with bauplane so constrained by phyletic heritage, pathways of development, and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. - G&L
G&L are saying that the many organismal traits are functions of evolutionary history, developmental pathways, and other structural contraints. G&L argue that most evolutionary biologists of the time did not consider the entire organism when ascribing adaptive value to any one trait. In G&L Panglossian metaphoric terms, evolutionary biologists had decided that the adaptive value of the nose was to support glasses, but they had failed to consider that the nose may have evolved for other reasons (e.g., smell) and that the supportive value of the nose was an evolutionar by-product instead of an evolutionary cause.
This brings us to the second metaphor, the architectural spandrels. Spandrels are triangular spaces that form when two arches meet, or when an arch meets a rectangle. According to G&L, spandrels are a necessary by-product of the architectural joining of the two shapes. The spandrel itself serves no purpose. In evolutionary terms, spandrels have no adaptive significance that resulted from natural selection. Instead, they are an evolutionary by-product that resulted from selection on other traits (arches and rectangles).
While the architectural metaphor apparently fails, their primary argument does not change. Traits cannot be considered individually. Traits of an organisms must be evaluated as one part of the entire organism, together with it's developmental biology and its evolutionary history.
Here are two examples to represent their argument, written for a general audience. The first example is based on the human hand. Our hand has five fingers. Each finger except the thumb has three bones (called phalanges), which you can see easily when you curl your finger. The thumb has only two phalanges. What is the adaptive value of having four fingers with three bones each, and a thumb with two bones? You might say that such a structure imparts excellent manual dexterity, from grasping to manipulating objects. But, would we not have that same dexterity if we had four fingers, or six? Why does the thumb have only two bones and not three? How could that be adaptive? These specific traits may not be the direct result of natural selection.
The structure of our hand is explained by our evolutionary history. Our primate ancestors had five fingers. So did our earliest mammalian ancestors, as did our earliest reptilian ancestors. However, some of the earliest amphibian ancestors, such as Acanthostega, had more than five digits (toes, fingers). Somewhere in early amphibian evolutionary history, our ancestral lineage converged on five digits, and most descendant vertebrates retain that five digit pattern. Even those vertebrates today without five digits usually display five digits during development, such as the ostrich (scroll down to image of blue-stained bones). If we assigned an adaptive purpose to the human hand independently of its evolutionary history, we might very well be wrong. Science doesn't like wrong.
Think about the five toes of your foot. Each toe has three bones except for the big toe, which has two bones. Manual dexterity? No. Evolutionary history? Yes.
The second example is the groove in your upper lip below your nose. This groove is called the philtrum. Can you think of an adaptive function for the philtrum? You might think that it helps to direct odors towards our nostrils, or hypothesize some other adaptive purpose. However, it appears that the philtrum is a by-product of the development of our embryonic face (YouTube video). The trait of our philtrum may not have adaptive significance. It is a by-product our face formation when the two sides meet in the middle.
G&L's publication produced quite an uproar. It's easy to find criticisms of the paper. Some have criticized the architectural metaphor. A bad metaphor does not necessarily make a bad scientific argument. Others have criticized the scientific rigor of their arugments. This blog entry, associated with the respected ecology journal Oikos, dislikes the paper and identifies several problems. The Oikos blog also links to several other sites that either support or dislike the G&L article. Most evolutionary biologists disliked the claim that they did not see the "whole organism."
Rightfully so, I think. I do not know of one evolutionary biologist (myself included) that has ever considered a particular trait without considering the broader evolutionary history of an organism. Indeed, considerable effort is spent by evolutionary biologists to determine how the evolutionary history of an organism influences its trait. The same applies for evolutionary developmental biology and other biological processes. For example, Martin et al. (1993) related evolutionary rate to body size, metabolic rate, and generation time of various animals, a very integrative (not isolating) approach.
To be fair, I think the G&L paper needs to be considered in the context of its time. Remember that i was published in 1979. Reread the first G&L quote above. They say, "during the past forty years." The G&L paper was published in 1979. Forty years before this paper was published was during the "modern evolutionary synthesis." Without going into details (ask another question on Biology.SE!) the modern evolutionary synthesis provided the genetic mechanism (and so much more) that explaiend how Darwin's concept of natural selection could actually work. Once the relationship between Mendelian genetic inheritance and natural selection was proposed, many evolutionary biologists tested this connection. It is not surprising to me that G&L perceived this strong "bias" towards a selectionist (Panglossian) paradigm because many biologists of the time were trying to understand how Mendelian genetics contributed to natural selection.
At the time of the modern synthesis, the structure of DNA was not yet known. The structure was finally realized by Watson and Crick (and Franklin!) in 1953, only 26 years before G&L's paper. Today we think nothing about the DNA structure but molecular genetics has advanced so much since G&L's publication that we have a much greater understanding of evolution and natural selection at the genetic level. Today, you can't study the evolution of a trait without considering its underlying genetic architecture.
In my opinion, one of the most, and perhaps the most, important development in the field of evolutionary biology is the field of evolutionary developmental biology (evo-devo). This field did not really mature as a discipline until about 2000, when the Proceedings of the National Academy of Sciences in the US devoted an entire issue to the topic. Developmental biology was a discpline that G&L had argued was important to consider. I'd bet that even they had no idea how important the evo-devo discipline would become to understanding evolutionary change. Still, recognition of the relationship between evolution and development was recognized as long ago as the mid-1800s by Ernst Haeckel. Evolutionary biologists were not necessarily considering traits in isolation from evolutionary history or developmental biology.
In the end, G&L used broad brush strokes to paint evolutionary biologists into a small canvas, claiming that biologists had a narrow evolutionary viewpoint. The evolutionary biologists responded (then and now) that their perspective was wide, even when focused on a particular trait.
The G&L paper continues to prompt considerable debate, which I think is the value of their paper. Every young graduate student should be required to read the paper. Even jaded scientists need a refreshing jolt to an established way of thinking. Our thought processes will alway benefit when we are reminded that evolutionary biology is a broad discipline that must embrace many other disciplines to arrive at a full understanding of the history of life on Earth.