Trading Perk for the #2 pick would be an equally big blow, in my opinion. The difference between Perk and Thabeet is gargantuan.
Actually, it's only about 4 inches.
Seriously, though, I completely agree. It takes a long time to develop a PG, but it seems like it takes even longer to develop a big man. Look at Oden. Even Bynum was relatively ineffective in the playoffs (at least relative to expectations).