Gilbert's drop in performance can't be solely explained by having a minor program or by riding clean. It's not that he's not at his 2009-2011 levels - he's worse than when he rode for FDJ right now. There's got to be more to it.
It could be a Mayo-like scenario: maybe he had to cut down on the program and then he put too much pressure into himself, thinking he wouldn't be able to perform; in short, maybe he became psychologically dependent on the dope. I believe that's partly what happens with Cobo, too.
But that's still not the only factor, and judging by the way he's fought even when obviously not in form, it doesn't seem like Gilbert is the kind of rider to go through that. While the lack of proper fuel may well be a factor, I'm more inclined to think of a botched winter preparation by partying too hard (in Monaco, with Hushovd). Maybe he let his success get to his head and he thought he'd stay at that level just like that, because he's that good.
There are many variables, and dope is a very important one, but not the only one.