It's a viable concern. Like you said, a few years down the road it's going to be tough to fit everyone under the cap.
That said I feel like he's being aggressive in this instance, but once he gets his guy under center it's easy to slow down a bit. Getting a QB, as I'm sure you know is costly. It's going to cost you either a season of having a bad football team or will cost picks/players to get there.
It's fair to wonder about the future. I like to believe that in the grand scheme of things that Beane will get it right. Win now and win later is what he has preached...and demonstrated.