Oh goodness, faithy. What a hard and horrid situation.
Is the medication something he will be on forever? Would it e possible for you to go to the doctor alone or research alone how side effects tend to play out in this sort of situation - whether it's an adjustment period thing, or a permanent change to character.
Then I think I would say that even if he is sceptical about couples counselling I would hold him to it. The scepticism might be posturing, or it might be something overcome during sessions.
Also, you've been through so much recently that I wouldn't be at all surprised if that is playing a part as well, possibly in you and how you perceive him, just as much as in him, and I bet couples counselling will help with that.
As for the God thing, it is such a personal thing that I don't really k ow how to address it, but I don't know anyone who hadn't had ups and downs in faith, and in a lifetime together I think it would be exceptional if neither of you went through it. Is it the kind of thing you could talk to your priest about?