Apocalypse has had a strange relationship with the X-Men for a long time now. I'm a new reader but I did read like wikipedia and stuff or a while now. I can swear I remember hearing about how he was revived after House of M because of his role as strengthening mutantkind. He helped forge them into something greater or whatnot and the 198 remaining mutants needed that.
So it's not like he was always just a force of pure evil, even to the heroes.
There's also the fact Moira sought him out. He was one of the "paths' she attempted, and which failed. No doubt she convinced him the way she convinced Charles and Magneto. She literally has proof what he was going to try to do wouldn't work.
I don't care what anyone says, Krakoa Apocalypse has been my favorite part of the era so far in what I've read. It's not like he's actually repentant for what he's done in the past -
There's just a better way now