Yeah, he did. This was not ALIEN 3 in that regard. If he was handcuffed, it was only really the script (in which case only some polish drafts could be done... and were... because the only alternative was to stop production and start over) and the score.
It just seems to me a lot of what some people complain about are script-related things. It's easy for those who don't like Zack to say, "Well, he's the Director, so EVERYTHING is on him", but that's being obtuse. If you have a problem with the way the film was shot, the way it was staged and blocked, the action choreography, the actors, the overall editing... yeah, that's him. But the script and score? Go pound sand.
People blaming him for Zimmer's score in the movie particularly annoys me. Because if there is one thing Zack does better than just about anybody, it's marrying music with motion imagery. It's been his bread and butter his whole career. He didn't all of a sudden lose those skills on MAN OF STEEL.
In fact, the temp score he cut in on earlier edits of the movie kicked all kinds of ***. And his initial idea was to actually ask Williams to come in and write a NEW Superman theme and score for a new generation, but that was immediately shot down by Nolan who had his boy Zimmer pegged, probably before even Zack was brought onboard.