They'll probably milk the rift for a good while but I'd be shocked if they didn't make up eventually. At the very least I would be surprised if they actually had the two groups at permanent odds. I'm imagining a situation where there's a timeskip, its quickly established that tensions have been there between the Rick/Michonne and Maggie/Daryl/Jesus groups ever since, and the first half of the season deals with that. They'll be forced to start working together again though with the slow introduction of spoilers:end of spoilers
the Whisperers