It's a "manchurian candidate" type thing, so I think it's plausible. I never honestly had a problem with it. I'm sure the more independant the Clone, the less likely they are to follow the order, but the true independant Clones are the ARC's, perhaps the Commandoes... Commanders are trained by ARCs, according to EU, but they're not ARCs. They're still the more simplified Clone design.
I really like the "Manchurian Candidate" comparison. I think that's a good way to look at it.