Interesting take above... Cable actually already defeated Apocalypse in the present, preventing the High Lord ascension and his rise to power that created the future he was raised in. So technically, Nathan has already won his war with En Sabah Nur.
Now... I'm assuming some animosity would still linger, considering he spent most of his life fighting against him and his evil. However, with Cable understanding that A) he's already prevented his dystopian future timeline and B) that Apocalypse being reunited with his family puts him on a very different trajectory (particularly if it's one that is beneficial to Krakoa's interests and mutantkind in general), then perhaps I could see him adopting a "live and let live" attitude towards his former mortal enemy.
Of course, I've not seen anything indicating "B" above... yet. But we'll see I suppose.