Two points:
First, Even though McNabb has been with Reid for ten years now, and is considered Reid's guy, it seems to me that Reid doesn't communicate very well with McNabb. As examples, the benching in last year's Ravens game, and last night. Reid could have very easily said to Donovan before last night's game, "Hey, we are going to use the wildcat quite a few times, because I want to see what Vick can do, and I want to give opposing defenses something to worry about. I want to do it tonight, because next week most of the starters are sitting out. What do you think?". Then you wouldn't have McNabb crying about it after the game. Of course its possible Reid did communicate with McNabb and McNabb is just throwing Reid under the bus. However, I don't see much reason to do that.
Second, I think the Eagles ran the wildcat quite a few times last night because the starters were playing, and that is who Vick will run the wildcat with in the regular season. Like I said above, they won't get much of a chance to pratice it next week because the starters will most likely be sitting out. I am sure they only showed the plays they did last night to get opposing defenses something to thing about, and the Eagles will probably do different things in the regular season then they showed last night.
I always thought McNabb handled himself well with the press with the various controversies that have come up (TO, Rush Limbaugh), but he has gotten very whiney in the past couple of years. I find it interesting that he said he lobbied for Vick, that he was excited about the wildcat possibilities (he joked about lining up as a WR) and the first time they practice it in a game (the only preseason game they will get to practice it) he complains that it is disrupting the offense. I like McNabb as a QB but after 10 years in the league he comes across as a little thin skinned. Maybe, as I said above, it is because Reid does not communicate well with him.
Overall, though, I don't think this is a long-term controversy, as both Reid and McNabb depend on each other for success this year.