I can't believe Fiona, the one who didn't want her people to become part of Tevinter's army when Alexius brings it up, who says she doesn't want her people involved with the Corypheus' plan to become a God and revive Tevinter to take over the world when Alexius talks about it, who hates Darkspawn and wouldn't serve one especially after her encounter with the Architect in The Calling (she was one of the few people in the book who was fully against allying with the Architect), would just agree to attack Haven unless she was brainwashed or broken into a mindless attack drone by the Venatori.
I think her even agreeing to the deal if kind of OOC for her since she was a sex slave for most of her childhood.
I think you miss the crucial part. She was molded over some more time and some of "her" mages were actually agents AND they were fed false information by an idiot Fereldan noble (arl or bann, I can't recall atm)... Basically, she was scared into accepting the deal that got pretty much altered later (that or a very fine print thing

) while remaining (along with other mages) under Tevene influence and in fabricated "situation" for quite some time already.
I still think she caught the infamous Idiot Ball, but she was being manipulated in more than one way at once. Then she made a deal. Then they kicked out Taegan. Which was quite a smart move by Alexius for a couple reasons, seizing control is one thing, but antagonizing Ferelden is another. When Fiona relaized they were pretty much conscripted to fight someone's war it was already too late - they REALLY had no friends anymore. Ferelden was hostile or soon to become hostile, Temolars were somewhere there even if the threat wasn't as big as she was led to believe, they already "allied" with enemy of the Inquisition and in then there were also real Alexius's subordinates there, taking control...
They were in a pretty desperate position. If we are to believe Dorian, some managed to run away, others were killed in the attempt. And Alexius in the all-too-well-known manner of "I altered the deal, pray that I don't alter it any further" were pretty much the only option other than (possibly fatal) attempt at escaping to become a fugitive in the world where the mage rebellion lost. That's pretty much the situation Fiona was in. Run and abandon her people or grit her teeth and attack fledgeling Inquisition HQ (note that while there was this Haven village part, Haven can hardly be called a civilian target at that point of time).
Basically, while it is all somewhat... far-fetched and Fiona did apparently not only get possession of but actually swallowed an Idiot ball, this doesn't really require mind-control to have a bunch of scared people pressed into military service and added to an army walking to take out some enemy outpost.
In fact, I don't think even Templars were at that point completely insane or mind-controlled. "Look, Inquisition allied with rebel mages, let's purge them" - for Templars even without their minds clouded in significant way that would sound sensible. After all, they broke off of the Chantry to hunt Rebel Mages. Now they go hunt Rebel Mages and their allies - allies who actually were already condemned by Chantry as heretics so even the more pro-Chantry of the rebel Templars could feel the warmth of doing Maker's will with Chantry approval...
I don't say Red Lyrium didn't drive them insane eventually, but I don't think that was really the central issue at that point. Though it likely helped a bit.
Clarel doesnt get any hate for a few motives, she repent her mistakes, helps you and she died to protect you.
Fiona doesnt repent her mistakes and even try to justify it, she does nothing, just stay complaining about your choices in the library and its impossible to punish her if you think she is guilty.
While I don't necessarily agree with some the things you say here, I think you are spot-on here. It's not that people hate Fiona for her stupid mistakes, even less - for her motives. The problem is, that she makes terrible decisions that make many people (including those she should protect) suffer... and if you side with the mages, she pretty much gets away with it. She doesn't earn redemption by death, she doesn't even break under weight of her mistakes and you can't punish her in any way. She doesn't really do anything that could earn her Player's sympathy back and many players (me included though I really am pro-mage in all this mess) can't shake off a distaste that this idiot, despite all the disastrous mistakes she's done and drawn her people into, pretty much wins if you side with the mages. The only defeat she suffers is possible depending on the Divine later on... but that's - again - the mages paying the price, not Fiona personally.
I don't say I would definitely opt to punish Fiona given the chance. But I would want the option of letting her go to be an unprecedented act of mercy, not a goddamned default I can do nothing about! It's like her mistakes literally can't catch up to her if you side with mages. And that's making people hate her so much. That's what makes me hate her. And I'm someone who spared (and never hated) Loghain on my first DA:O playthrough despite no knowledge of his background. I just played a merciful Warden. But I COULD punish him. Not punishing was something done after acknowledging his guilt and despite it. Fiona? Fiona is left as the leader of the mages and everyone - Inquisitor included - is somehow ok with it.
It doesn't surprise me one bit that people are furious and let their steam off on BSN.