Bacteria to Destroy Greenhouse Gases
The problem of evolving systems is a difficult one, especially where the unanticipated consequences may have disasterous results. One solution that I've heard mentioned is that we might engineer exotic environments to contain the microbes (or algae, whatever).
If the bugs require the exotic environment to survive, then if they are released either accidentally or deliberately, then they would die. In this case, that might mean finding slime that dies at lower temperatures, enclosing the smokestack, and maintaining the 130 degree temperatures that the algae needs to thrive. If they escape, they die.
This does not necessarily resolve the problems related to mutation of the original strain; but if the mutation required is significant, then perhaps it will delay the issues sufficiently that our clean-up capabilities improve enough to handle a relatively specific danger.