No that episode did happen, the warship voyager stuff was an erroneous retelling of events on the part of the aliens, but that version of the Doctor absolutely still exists and could appear at any time should the writers decide it so

It doesn't need to do any of that, it's not trying to be like traditional star trek, people need to stop locking down franchises under specific rules and expectations, it's an entire universe of possibilities, let it do new things.

As for the defiant being there, no that doesn't make sense, why would a random presumed dead terran have access to such a prized ship? Not only that but the attention from actual starfleet that might generate would be problematic. If there was to be a classic ship appearance, it should have just been showing Lt. Garrett returning to starfleet and have her board an Excelsior or Miranda class. That or have a character name drop the Enterprise B. But outside of that keeping Starfleet and the federation as off the table as possible worked for the movie, and personally I hope we get future movies that focus on other elements of the star trek universe, a Klingon central show for example would be amazing.