Yes, you have a point, but notice that the most benefited by that society are the pure-strains humans. Mutans can likely survive without making new mutants (I mean the individuals, not the race, I don't find a reason for they to want to perpetuate the race in itself), so they don't need to work to maintain a constant flow of pure strain humans to get more mutants. Humans might be motivated for that because it's biologically more difficult for them to survive in the wasteland (they'd really need society), so having a constant flow of mutants working with them might be an advantage, and since they DO reproduce, they might want to form a family and give sustain to them. Mutants can't, so they would probably just want to watch for their own individual survival and freedom. Of course, they might want to have a purpose which motivates them to keep that society going. Humans could agree to that just because it ensures survival for them and their families. Anyway, my point is this can be a good experiment of a faction if we find a suitable purpose to make the mutants want to be part of this.