When I was reading this at the time it was published the breakup of Peter and Kitty looked to me like payoff from a line/piece of foreshadowing in the 'Days Of The Future Past' arc. The remaining X-Men are about implement their plan to change history; Peter draws Kate aside and asks she really wants to go through with this because of all the other changes that might happen, including the possible negation of their relationship; Kate counters that saving the lives of millions is more important than their relationship; and Peter smiles and says "I am selfish. It matters to me." This was when Claremont was noted for his long term subplots and was just about to get the reputation of going insane with them, so it looked like it was planned.
Then years (no, wait: decades) later I read that it hadn't worked that way, and IIRC that it was due to Shooter's intevention, and taking into consideration the editorial inteference that led the the reworking of the conclusion of the 'Dark Pheonix saga' this seemed plausible as well.