The guide is not canon, and Patrick himself wrote he was not sure about it and he assumed it maybe right, he told superdarkone to ask David Gaider. If he said "yes it is correct" this discussion would be over.
But even if they were brainwashed, there is not indicating it in game, look how many people dont have this impression, the only place its mentioned is in the guide.
But it makes no sense. The Venatori never seem to register the fact that they have Redcliffe mages in their ranks. From my knowledge every letter about them is written by a magister and there's no codex or bit of lore that tells us about the rebel mages decision to join the Venatori or their reaction to Corypheus. They just do so seamlessly. We never see, hear or understand the reasons behind that decision beside them having that deal with Alexius, which turns out to be utter bullshit anyway so why would they continue to adhere to it, especially once they find out that their new boss what's to destroy the world.
Brainwashing seems to be the only answer to this problem because it would actually explain why the entire mage rebellion would just give up what few morals they had and join up the very embodiment of why people despise and fear mages in the first place. The Templars turning evil made sense in the game because they were manipulated through their addiction to lyrium and because their senior members were all converted already. Looking around Redcliffe you see that the mages aren't exactly thrilled by their "alliance" with Alexius and Fiona herself hates the deal as well.
So, yeah, it's either a plot hole, bad writing or a missing codex, and since the guide actually gives an explanation I think it makes sense to go with that.
Love to see what David says about the matter though.