So I'm actually coaching middle school football for the 1st time this year, so hopefully I can shed a little light (although if we had a QB who could throw, we'd definitely want to utilize him). We're pretty much told to run the exact same offense as the high school that we feed into so they'll know the terminology and what the high school coaches want from them by the time they get up to the varsity level. Which is probably why they want to roll with the fast QB who can run. I'm really only pointing this out because it was kind of news to me when I signed on.
But like I said, if you're lucky enough to have a middle school QB who can throw the ball well, you need to find a way to make it work.