Scott had become aggressive, we can agree; the Avengers also had wetworks teams before, only they weren't trying to stave off extinction; he did not declare himself the authority on all things mutant, or did you forget that Logan left with a bunch of mutants and Scott didn't kill anyone for disagreeing with him?; he formed his country under a US that had Osborn as the top cop and he only promised retaliation to the nations of the world, last I checked plenty of nations IRL do the same.
The Avengers listened to Logan, who can't be said to be morally superior to Scott, and they're full of killers and former-killers. But sure, lets hold Scott to a completely different standard.
If all the heroes of the MU were behaving rationally all the time we wouldn't have so many events. The Avengers weren't exactly the most rational or moral heroes at the time either.
They wouldn't have had that power if not for the Avengers; no one would have been hurt if they stopped attacking the P5; and the Phoenix was not going to be stopped, so the Avengers are responsible for the P5; and lastly, if Marvel wanted readers to question the viability of the Phoenix, it should've been done in the lead-up to the event not during.