He may or may not be standing up for the consumers. Recall his reasoning for making stylistic changes to some of the characters for the movie wherein his answer was sometimes, "Because I wanted it that way..." Also, remember the way he took the criticism from the fans.
I'm not saying that the reason he wants to cut ties with the company
isn't because of principles, I'm just saying that he sometimes can be a little childish. It's
possible that he was already looking for a way out of Transformers 2 and that this 'out' allows him to look like a good-guy taking on the monster corporation.
Having a non-Bay sequel might be all right, after all. He did a nice job of playing around with the mythology, but he did some things that weren't exactly what the collective fandom wouldn't have wanted. Additionally, he really didn't include some things that would have been welcome. Think about this: Besides Prime and Bumblebee, was there any kind of character development for the other Transformers? Couldn't those characters have been Generic Autobots A-C and Generic Decepticons 1-4 or something? Could we have cut the 'hiding outside Sam's house' to 1/3 the length and developed these characters a bit?
That's a long-winded post. The take-home message is that Bay may not be the boyscout here and that (although I enjoyed the film) a non-Bay sequel might not be the worst thing ever to happen