The short answer is: unless you burn the sample completely to ashes, you cannot be sure you destroyed all BT particles.
Denaturation is a naturally occuring process and it works pretty much like radioactive decay. It happens over time, so if you had a solution of BT without any bacteria or spores and left it at room temperature, after some (very long) time the toxin would be destroyed. By adding heat (or acid) you accelerate the denaturation, but it still is a statistical phenomenon. If at a certain temperature half of toxin particles are destroyed within a second, it means that within a minute one in $2^{60}$ will be left. But 1 in $2^{60}$ is not zero. If you keep the temperature for two minutes, one toxin particle in $2^{120}$ will be left. You can never be 100% sure all toxin was destroyed.
This also means, that there is no one set "minimum time and minimum temperature". The higher the temperature, the lower the time needed. You can keep food at room temperature for a very long time and the toxin will be destroyed (though I doubt that the food itself will survive that kind of time).
On the other hand, one molecule of toxin will not kill you. Think about BT injections as anti-wrinkle therapy. A small amount of toxin in injected, it paralyses small facial muscles and the face looks smoother, younger. The effect wears off, so you have to repeat the injection every now and then. In order to make food safe to eat, you don't have to destroy all BT molecules. From a booklet Food Safety Hazards and Controls for the Home Food Preparer (2006 edition, available at http://www.hi-tm.com): a healthy adult can eat up to 1000 spores with no ill effects, Clostridium botulinum bacteria and spores are considered destroyed after 2.4 minutes at $250^\circ \mathrm{F}$ ($121^\circ \mathrm{C})$ - this in fact reduces the number of spores $10^{12}$ times and is called commercial food sterilization, the toxin is considered destroyed after boiling for 10 minutes but the temperature of $165^\circ \mathrm{F}$ ($74^\circ \mathrm{C})$ will not destroy it. This booklet also advises to boil for 10 minutes any homemade canned food if you are not perfectly sure the original procedure was appropriate.