How would you react if the game went like this:
Alexius: I'm changing the deal
Fiona: The Inquisition needs mages, then let's join the Inquisition and break off this deal
"Mages join the Inquisition"
No gameplay and we all know Bioware would rather make people hold the idiot ball than write a story that makes sense. Harvester Orsino on the mage side is just the most prominent instance.
Bioware could have still written an actual quest to follow Fiona ditching Alexius. He seems like a smart guy who is always prepared, I'm sure he would prepare for her defection once he showed his true colors. Why not have her join the Inquisition in the tavern, then he does the Tevinter mustache twirl and says he knew she would never fall for such a stupid plan, clicks his heels, yanks on the time amulet, and the entire tavern is pulled into the future.
Or something along those lines. Why would Fiona rejecting his offer automatically mean Alexius would meekly accept it and leave? He's not Fiona!
Yeah, he altered the arrangement *after* the deal was made and Fiona was bound to him.
This was the perfect time for her to reject the arrangement. He had proved he was willing to change the arrangement to suit him without prior warning, the Inquisition appeared as an alternative ally, they were outside of the castle with few Venatori around. But she just whimpers and follows him, knowing she is leaving the potential ally who wants her help in closing the hole in the sky in order to become slaves and presumably fight against the Qunari.
Fiona was never bound to Alexius in any way that infringed upon her free will. She was just as capable of altering the arrangement as he was- and has every grounds to, since he broke the agreement first.
Whether slavery, military service as canon fodder, and being a tool for a politician in a notriously oppressive and exploitative regime that pits its own mages into a dog-eat-dog politics is better than the Circle is highly questionable. Especailly considering what 'actual freedom' means in Tevinter.
Whereas her followers were not actually in danger of being wiped out by the Templars. The approaching Templar army right over that hill that I can save you from if you just sell yourselves into slavery now now now was a deceit of Alexius- and one Fiona fell for, hook, line, and sinker. There was no such Templar force- and no such Templar force could plausibly have overrun Redcliffe castle. We certainly have no evidence Ferelden was intending to withdraw it's already established offer of protection to the Mages.
So is losing a war and having your proud rebellion ground into dirt and reliant on the benevolence of strangers.
Which actually did happen, whereas there's no indication that blood magic was ever involved, and if there's anyone involved who should want to be able to claim 'blood magic' as an excuse for their actions, it's Fiona. But she doesn't..
Yeah, the blood magic theory is fine, but it's just a theory. Bioware is usually not very subtle about things. If blood magic had been involved, Fiona would have mentioned it in Skyhold, or there would have been a cutscene between her and Dorian about it, or any indication that blood magic was in use. Not theories that are weak headcanons to justify poor writing.
Bioware would have at least had some hint, like the soul swap Cory did at the end of Legacy oh wait people still didn't believe that was a clue never mind.