The antagonist and the protagonist could be good guys, both working for the good, but at odds in how to achieve it. The antagonist might think the protagonist is the villain, only to find out (usually, almost too late) that he or she isn't.
What you've just described is a major part of the Girl Genius story.
My need is for a early 'side trip' obstacle for my protagonist(s), a sort of pons asinorem. I think I've got it now, by reworking and cutting what I've got now, and filling the matter in while a clock ticks somewhere else.