In the previous installments of Captain America, Steve Roger's (Chris Evans) morality was never questioned even though he was defying orders (especially if he was defying orders). He indisputably did the right thing by rescuing Hydra POWs, one of which was his best and closest friend Bucky Barnes (Sebastian Stan). He also did the right thing by taking down SHIELD and Hydra in one fell swoop. Here, he is the crux in the split of The Avengers, not because he rejects the Sokovia Accords, but because he wants to protect Bucky from being framed. It is perhaps the first time Steve's morality is called into question. And it should have been done better.
You've probably heard it before and I'll say it again, the idea of the Marvel Cinematic Universe is an unprecedented feat of filmmaking that I can only assume requires a lot of organization, a lot of discussion of what is canon and what is not, and clearly defined goals for each and every movie that comes out of the Marvel/Disney machine. The directors for these films work closely with the producers to keep the movie in line with not just the Marvel overlords but also the characterizations of each superhero that appears on screen.