Yeah. I'm not planning to add this soon, but there's an idea you could take the evil path: striking a deal with Mercs and throwing away all this 'defend the mutants' thing, become for-profit-only evil pirate. I was planning to do it like this:
1. optional research that enables a new mission spawn
2. mission (do a Pogrom... yourself, and get paid)
3. you get research item
4. once researched, this changes missions that spawn - in short, no more Mutant Pogroms in the defensive sense, now you go to kill and rob the mutants.
5. this should make it impossible to form Mutant Self Defense Force or help mutants in other constructive ways;
6. However, even if these actions will be based on missions too, and these missions would be blocked by research, the player can hoard a research item and research them both later, at the same time, thus weaseling out of such a choice.
This is only a general outline; it's possible there will be more of such game-altering choices.