At this point I think it might be that Anna got sent as canon fodder...she might have thought she was doing her own agenda, but Michael&Co knew what was going on the whole time.

Although this does make me question Michael's pronouncement about Free Will. I mean, Zachariah did show Dean a future where Dean never said yes, right? So...Free Will did exist (for better or worse) in that timeline. Either Zachariah is screwing with Dean, or Michael is (or both of them, quite possibly).

But then again, plot holes in SPN? What?