There's also something in the Hissing Wastes that also changes based on whether or not you're siding with mages or templars, since it's the Venatori acting in that area.
I may be misremembering, but I'm pretty sure that it's said that all the mages who disagreed or refused to follow Tevinter were killed by Alexius, if they didn't manage to escape.
I also think there's some dialogue if you side with the templars you can eavesdrop on in Redcliff. Need to go through that again though to confirm.
I think it comes down to one simple fact. The rank and file of mages and templars both got the shaft from their leaders. One had them join Tevinter, when 2/3 we talk to in Redcliff hate it, but they get killed if they don't escape or don't agree to serve, and the other side had its leader willingly allow an Envy Demon to take command and slowly corrupted the templars with Red Lyrium while he went about trying to destroy the entire Seeker order.
I dont remember the codex in the hissing waste, but I remember a banter between Bull and Dorian saying it.
If the Venatori plans was to brainwash the mages, why Fiona wasnt brainwashed in the future?
It appears I don't have a savegame to be able to access that certain war table mission but thankfully its available on p. 39 of the official guide. Quote:"If the Inquisitor chooses to meet with the templars instead of the mages, then Fiona and her compatriots would be brainwashed by the Venatori and used in the attack on Haven, in which the Inquisitor is forced to kill her."
Yeah I know about the guide, but this guide is full of errors, I wouldnt be surprised if this information is more the author interpretation than actual fact.
But I will concede that the rebel mages could have been brainwashed, but in my interpretation (until I find some proof), is that Fiona attacked he Inquisition willingly.