Tend to think that comments like that are more used as insults than statements of fact/supposition.
Suppose it all depends on the nature of the Cylons' brains/decision centres, or whatever they've got, doesn't it?
A lot of the evidence we've seen to date suggests that the human-Cylons are organic in every way, from the data Baltar gathered from Leoben's corpse in the mini, to Caprica Boomer's pregnancy by a human and everything in between.
It thus follows that "programming" the human-Cylons may indeed be a type of mind control/brainwashing, rather than the sort of procedure you'd carry out on an electronic device.
It probably also explains why there appears to be individuality within the Cylon models, and also why the programming method appears to be imperfect at times.
Variety of potential explanations for that. The impression I had was more that Gaeta admired Baltar, or felt like he was sticking up for his buddy than anything else.
What you suggest is certainly possible though. The problem at the moment, as Adama said at the beginning of the series, is that if Cylons look like us, any of us could be a Cylon. Still plenty of room for sleepers and saboteurs, until we've met all the models of course...