As far as I remember, Sara's renewal negotiations were undergoing at the time the finale was filmed. And between that time and when the episode aired, Sara decided to leave/didn't like what they offered her and told Shonda. They left an open end for her story, she left so Callie stayed in NYC; if Sara would have stayed, Callie would have come back and probably patch things up with Arizona.
Patrick and Sara's departures were mutual decision and this time they are firing them (not renewing their contracts; same thing) but it does seem there's no bad blood; every actors knows that can happen anytime. And Shonda has a deal coming with Netflix, maybe we'll see any of them popping up in the new Shondaland shows.
But if the reason isn't money, good lord get rid of those interns no one cares about and they don't even bother to give a storyline too. April and Arizona have been around for 10 years, but you can still give them things to do: I'm enjoying April this season, Arizona seems to have found something to stick to with this study.... Not to mention Arizona has a daughter living with her and it'll be nice to see the woman who changed her mind about having kids deal with being a single mom AND dating.