If you're not going to give him full credit for scouting prospects, you can't give him full credit for scouting free agents either. As far as budget management, I think he has done very well. How many homegrown players have the Red Sox not been able to afford to give contract extensions to? Every year, 10-20 million comes off the payroll, and every year that money goes back into the system.
The Red Sox have the second best group of homegrown players in baseball right now, according to WAR values. I think that's worthy of an A in drafting.
And despite his failures with FA signings, pretty much every big trade Theo has made has been gold, with the exception of Gagne.