Also, Dark Phoenix in X-Men #137 was on the verge of being lobotomized by the Shi'ar as punishment for her actions. "She" was saved from this fate by committing suicide. That's a pretty heavy price to pay - what price will Scott pay? And for that matter, what punishment awaits Namor, Colossus, Illyana, and the White Queen?
Just to neutralize her so she'd never pose a threat again.
Otherwise, the Phoenix could have risen once more.
I think the Phoenix theory has evolved since then so them becoming Phoenixes again is probably not a consideration this time. Escpecially since they got it by accident.