I hope it won't be raining when we leave church
I hope it won't rain when we leave church
I can't see the difference. For me both mean the same thing and I think first one is better.
The second one is not a general statement and a rain has always a beginning and an end that always last longer than we would like, so "won't be raining" seems to be better.
After thinking of it the only difference I see is that in the first sentence the rain has begun before we have left the church and in the second sentence the rain has begun while we are leaving church.