Is it conceivable to influence the course of their evolution so that it becomes more likely they gain the intelligence to support a civilization in the distant future?
No, I don't think so, based on what is known about evolution.
Your idea is in keeping with the opening of Kubrick's 2001: A Space Odessey, where the monolith inspires one of the primates to see a femur as a weapon. He picks it up, hits an opponent with it, and the idea catches on within his group; the implication is that this inspired male's (female's?) group goes on to domination and are the progenitors of the human race.
In real life, that's not how intelligence is passed on. You can teach a gifted bonobo how to build a fire, but if he's not into roasted meat, or really cold, or trying to scare away predators (or if he doesn't realize that's what fire is good for), all you have is one bonobo who can start fires. It doesn't influence his genes.
To actually influence evolution of bonobos, I imagine it would look like this: You capture 4/5ths of all the bonobos in the world (leave the 1/5 for genetic pool variation). You test them for basics of quick-wittedness. Kill all the bonobos that fall below a certain threshold, and release. Repeat several generations later. Keep doing so for 50 cycles. What you will have are a race of quick-witted bonobos - maybe. Because if the quick-wittedness you selected for doesn't provide them with a survival advantage, it (and they) will die out. What if the smarter bonobos all want to be alphas, and all that fun cuddling and sex-as-peacekeeping were to disappear? They might not survive the bonobo-chimpanzee wars, because they won't live in large, peaceful, cooperative groups any more. Maybe you can teach the bonobos to plant crops, assuring a food source. Will they irrigate, too? What would this decrease in roaming mean for pygmies who hunt bonobos for food?
My point is, we can't control evolution very much unless we also control the total environment they live in. That's one way we have been able to have such an impact on a rather extraordinary species: dogs. But in the end, a dog, whether it's a sheep-herding or rat-catching or boar-hunting or bull-baiting or duck-fetching breed, is still only a dog. Invaluable helpers, but after all that selective breeding, they're just dogs. The smartest dog in the world still likes to play fetch more than anything in the world. Even eating, if she's anything like my two Border Collies.