You know... it wouldn't bother me if it isn't.
Bear with me, I know that sounds weird. Just trust me here.
First, ever read the classic Batman story "The Killing Joke"? The basic story is that the Joker wants to prove to Batman that everybody is just one traumatic moment from becoming just like he is- like THEY are, since he suspects (rightly) that Batman got the way he is the same way. So, he tries to make Jim Gordon his demonstration piece by shooting his daughter. It fails, in the end. But here? Ward actually seems to have (for now) proven The Joker right- because he gave Phil Coulson a very bad day, and Coulson has SNAPPED. I'm fascinated by that- I'm sure the Joker would be as well.
But, that aside. So Phil has gone pretty loco, and that leaves him up in the air as far as his status moving forward as director, even really as a useful member of the team. So what? If this was last season I'd be screaming to get Phil back to normal, but now? I think they could do this without him. Not that I'd WANT that- I love the character, and of course Clark Gregg is contracted for the foreseeable future to be in this thing. But if he left right now, if Coulson handed in his lanyard and sauntered off to do something else with his life, I think the team- and the show- would do just fine without him. They've built their cast out into something that could survive it now- the characters have backstories, motivations, personalities all their own enough to make it happen. Really- attempting that midway through last season would have been the death of the show, but now that we have so much more established for people like Mack, Bobbi, etc., to say nothing of the season-1 people like May, it's possible they could pull it off, make Coulson into a background kind of guy the way they sort of have with Daisy/Skye, and leave it at that moving forward.
...Of course, with The Warding Dead now on Earth and Malik's plan (whatever it is) moving forward, that's not going to happen, but it's intriguing to consider, at least.
(Also, am I the only person who hopes Coulson makes an appearance in Civil War, if for no other reason to just let Stark and Rodgers know "Hey, actually I'm alive, and you're both acting like idiots. Just sayin'.")