I for one don't think they had this coming. Hell I don't think this should have even happened to them.
I actually really do see Cyclops actually believing that the Phoenix could be controlled, with proper training that is, not without risk but it was possible. Also the only other reality would have been to face fact that a cosmic entity like the Phoenix would destroy the earth. Hope being prepared was his number one priority and later keeping her safe. The only real flaw in his plan was that she (Hope) didn't share his conviction, thou that seems to be changing. Well that and the fact that the others of the Phoenix 5 could control the bird like he has. Cyclops after all is all about control, self-control.
Emma is Emma! She does things her own way but her end game is, and has for the longest been, protecting mutants. She became the head-master of Xavier's school because when Cyclops had closed down the school as a result of Jean dying. Emma was determined to continue with the school on her own without Cyclops, if he so chose to. He became co-headmaster, not the other way around, lest we forget it was Frost International that financed the rebuild later with Worthington backing. She is weary of dealing with the Phoenix but stood with Cyclops because of his conviction.
I love(d) Jean. It's sad that Emma & Scott get slammed for their telepathic affair when Jean was pretty much doing the same thing with Logan, for far longer. IMO that is one of the reasons Logan gets where Frost was coming from, they were in the same boat. It would be nice if Jean could come back and stick around this time. if for no other reason than being with her daughter and maybe finally have an honest go at having a thing with Logan.