The major difference is that mutants are constantly on the verge of annihilation. The X-Men trying to be the peaceful heroic types while those stories are being told comes off as them not being aware of the reality they're in. You can't talk down a Sentinel. You can't just arrest the Purifiers or the Reavers. The only way the X-Men can afford to just be pacifistic heroes is if mutantkind isn't on the brink anymore.