digger, there's no discrepancy between the movie and Seven. The intention of the episode was to describe conspiracy theories, which they did. Uhura and Spock plainly said what they were meant to, too.
I would first like to state that I do agree with you that this is, in fact, an alternate relaity. The part that I disagree with is that I don't think, by what is on-screen, all viewers MUST think it's an alternate reality.
Granted, it's the conclusion I've drawn from the information at hand, but, in my opinion, no where on screen is there any definitive proof. The only mention of "alternate reality" on screen is during a discussion about a possible explanation of what is going on. This isn't a fact that the characters extrapolate from proof and test. It is only a theory, mentioned during a single conversation, as a possible reason.
As a result, it's not absolute. I would agree that there's every reason to believe that after the "Nero incident," perhaps the Federation's greatest minds got together and did prove it. But it's equally as likely that they got together and disproved it. It's left up to the viewer's interpretation.