The eldar would definitely kill them, given that mutants are pretty much exclusively chaos corruption now (RT era, mutants were from nuclear, biological and chemical exposure).
Dark eldar, of course, might cage them if they're interesting or dangerous specimens, for experiments and arena matches.
Tau...? I don't know if its ever come up. They'd probably treat it as a scientific or medical problem to be solved, provided the mutants weren't hostile.
Remove the worst of the mutated tissue and replace with grafts and/or implants. For problematic mutants, the greater good would be the gun.