Trust me i'm no fan of the Shi'ar...but, and this is one reason why retcons suck(like that Rook'shir/Blade of the Phoenix/Blue Echo crap), it makes no sense if, "every" manifestation of the Phoenix results in "bad shit happening", they wouldn't have been so chill during the original saga.
Also, Jean aside, the Avengers still had to know of Rachel as Phoenix.
And lastly, when dealing with a cosmic force, "bad shit" is all relative. In the original story, before going off into Shi'ar space, she told the X-Men she was off to fulfill her "Malefic destiny". If she just wanted to eat stars, the sun was a hell of a lot closer...so why D'bari? Morrison's run added that the Phoenix "burns away what doesn't work", and also eliminating species deemed as obsolescent. To put it in terms of our own evolution, let's say a cosmic force nudged the fateful asteroid that killed the dinosaurs...horrible for them, yay for us.