She’s going to be resurrected. And the XMen will have a powerful enemy in her. I do think Xavier will be able to smooth things out, though and eventually she will join the council. But first the consequences you mentioned need to play out.
Emma, Mystique, and Destiny were too eager to undermine Xavier and Magneto. Those two would have pushed for Selene to be on the council.
No matter how bad she wants it, Emma will never be a leader like Xavier, Magneto, or Storm. She is simply not major league.
Nor is Hope. It is a lesson they are about to painfully learn.
Meanwhile, Krakoa didn’t just make an enemy against Selene. She was hanging out with Coven Akhaba, who will want to teach her a lesson.
Sinister will face consequences as well at some point. I suspect he goes in the hole and by then Selene will be on the council. We have to see how soon it is before she is officially resurrected.