It runs counter to everything we know about the Phoenix to have it be an evil, selfish entity from the start, and robs even more from the Dark Phoenix Saga than the retcon that Phoenix wasn't Jean did.
Phoenix was fundamentally neutral, I might even argue benevolent, in the final FF reading. It granted Jean her heart's desire...saving Scott, the X-Men, and herself as an afterthought...in exchange for getting to live through her, experience her feelings, emotions, and life. Byrne argues that it fooled itself into thinking it was Jean, where Claremont's hinted that Jean's soul may have been in the driver's seat the whole time. I prefer the latter, as it's closer to the intent of the original concept behind Phoenix as a character...Jean with a massive power boost.
To have Phoenix be an evil entity from the start just undermines absolutely everything that was tragic and compelling about Dark Phoenix. You have to be in a state of grace before you can fall from it.