I think it makes sense. The family schtick had pretty much run its course and was rapidly getting stale and it cramped his style. It was also pushing him in the direction of retiring from the serial vigilante business. It was good for one season but would have gotten in the way of the next one, whatever that will be about. I would assume that Cody and Astor will live with their grandparents and that Dexter will raise his son with a nanny who will pretty much leave him alone.
There are some loose ends remaining. Dexter is still facing jail time for fleeing the scene of an accident and now he has to explain why Trinity killed his wife specifically and WTF he was doing in Trinity's garage before the rest of Miami Metro arrived and if the family talks about this mysterious Kyle Butler person who ran out the back door as the police were coming in the office will go looking for him. He could also just dismember Rita, clean up the his bathroom, dump her in the ocean, and tell everyone that his marriage hadn't been going well and that she ran off.