The Mayor of Crestwood and Mistress Poulin of Sahrnia were also desperate leaders who resorted to terrible things. The Inquisitor could judge and punish them. The punishment varied from merciful ones to harsh ones but it was there. Fiona should have gotten the same treatment.
I am someone who is pro-mage and pro-Circle. My position is quite similar to Wynne's position. I think Fiona was an awful leader and out of character, given her experiences as a slave, as an ex-Grey Warden, as a Grand Enchanter and as a rebellious person. If Fiona was being true to herself, she would have given Alexius the finger the moment the Inquisition stepped in, just like how she was willing to give the finger to the Chantry and Templars in Asunder at a very tense moment by declaring Circle secession. For someone who was a slave, I find it hypocritical that she indentured herself and the entire Rebel Mage to Alexius, especially when you take into consideration that the Ferelden Monarchy have granted the Rebel Mages refugee status to seek asylum in Ferelden. All she really had to do if she was worried about Templars was to contact Arl Teagan for aid, since he is part of the Ferelden Crown or at least related to it and is bound to uphold the refugee asylum status for the Rebel Mages.
Honestly, I was disappointed we couldn't commend them for making necessary sacrifices. Betrayal or no, the Blight is the Blight. And Poulin's collaboration was a no-win situation- not doing business with the Red Templars once she knew the truth wouldn't have helped anyone, since at that point they would have/could have just abducted people anyway. She wasn't in a position to stop them.
It's not that I don't feel it's perfectly alright to condemn them- I'd just have liked it if for some of our judgements (like this one) we could judge 'not guilty,' or 'justified.' For the proven members of the Venatori, every option being a punishment of sorts makes sense. But for questions of whether it's really a crime, given the context? We can absolve the Wardens for worse.
And yes, I'd be more than open to the possibility of a 'not guilty' judgement of Fiona having that as an option if she were tried. Put in the relevant approval effects if you do, but by all means let the Inquisitor give pro-mage rhetoric and absolve Fiona of guilt because Templars. The Templar judgement of Knight Captain Denam allows you to sentence him to, well, being a Templar.
*I note we haven't actually mentioned Ser Denam much- and he is a Templar judgement in which the idea of 'just following orders' is raised. The charge isn't that he knowingly did anything bad- it really is that he followed orders that harmed and risked his faction. That's could be relevant to Fiona as well.