The X-Men (and mutant kind) have faced off over the years against a large number of genocidal bastards and lunatics over the years from both sides of the divide. they know, for a fact, that these nutjobs will win if left unchecked.
Thanks to the stupidity of M-Day, the flatscans have a non-trivial chance of exterminating mutants "forever".
And back in the day, whenever a threat was brought to the boil it'd show up, slaughter X number of people in a massively showy fashion and get seen off in a fight that inevitably caused hundreds of thousands, and more likely millions, in property damage and bad PR.
A pre-emptive black ops team isn't only the sensible approach, it's the responsible one.