> If you REALLY want them to self-terminate but you found out that they mutated and can now synthesize X & Y, you're in trouble.

There's a good hook for a sci-fi story. Some low-level manager in a biochem company starts siphoning off XY juice to sell on the black market, and doesn't realise that by slowly ramping up their thievery they're evolving the killswitch out of their engineered organisms...