Jean seems to be in real trouble too...that was unexpected.
Yeah it feels like at this point she comes back as Phoenix and most of her humanity won't be there for Cyke and the rest of the X-Men.
That's why I think those Jean scenes were significant - they're basically a send off to her for this era of X-Men. If it's like the comics, it'll be a while til we see her again as herself and not the Phoenix.
Maybe this is the way they bring in the Avengers to help stop a multiversal Dark Phoenix threat (not the omniversal WPOTC though) later on in the future.
They're doing a great job setting everything up.