I honestly don't think it's that big of a deal. I know harsh for me to say. But the PF had been slowly corrupting all of them - Emma was manipulating Namor at the time, and like she said "Our smallest ideas are ticking bombs, all primed to go off." She wasn't in total control of what was going on -- and like she said in issues before she needed help because she knew she wasn't able to control the PF and Cyke just walked away.
I'm not happy with what happened - I love Cyke and Emma together, but I honestly think it will just blow over and the two will get over it and stick together like they've stuck together this last decade.
I hope so, if she was possessed by the Phoenix Force at the time then she wasn't in her right state of mind. If Scott was able to forgive Jean for all the drama and destruction she caused as the Dark Phoenix, he should be able to forgive Emma for having an affair while possessed by the phoenix as well.