I'd still give Vick the nod against Brady, but it isn't clear cut because the stat categories are so different. Take out the missed time and go by average stats, it becomes more clearly Vick.
But why take out the missed time? That's part of football. Taking out missed time for MVP voting deemphasizes the contributions of the player who helped his team in every game.
Besides, even with their stats being difficult to compare by virtue of Brady being a pocket passer and Vick being a running QB, there's no way that Vick's season is "clearly" better than Brady's. Brady has nearly double the passing TDs, and a number of those came against defenses that were supposed to be elite (Steelers, Jets). Also add the fact that Vick is operating an offense with high picks at the skill positions (Jackson, Maclin, McCoy). Brady is operating an offense with two undrafted running backs and a retread Deion Branch. Brady is doing more with less.