Yes. Back in the 90s, Jean and Logan had kinda of resolved their sexual tension. It was still there, but Logan had decided to back off because she clearly loved another man and he was just toturing her. That allowed them to become good friends.
Then came Morrison's run... *sigh* I'll just say this, though: I don't read it as Logan rejecting Jean per se. I read it as he, finally, doing the decent thing, understanding that Jean was at her most fragile he'd ever seen her and if he didn't walk away, it would be the equivalent of taking advantage of her.