Considering Johnston said this
before the first movie opened:
Joe Johnston wrote:
I told the Marvel guys that there is a character that I’m really interested in called ‘The Winter Soldier’ and that if, ‘you guys decide to make that picture I would definitely be interested.’ It’s the ‘Bucky’ Barnes story.
I'd say the fact that Disney is moving ahead with exactly this movie without Johnston involved doesn't indicate a great relationship between the two. Of course, it might just be a scheduling conflict...