I want to elaborate just a little more on the Tevinter alliance. I suspect that Fiona believed a long-term war was hopeless for the mages. Yeah, they could hide in Redcliffe forever, but then they are essentially right back in confinement all over again. What was the point of the rebellion if they end up trapped and surrounded by people who hate them? Alexius probably framed their circumstances in this way, and convinced Fiona that a decade of slavery in Tevinter with the promise of future respect and freedom would be better than hiding in Redcliffe for Maker knows how long, especially when they will be blamed for everything that goes bump in the night.
So Fiona lets the Venatori march into the village, unaware of their true motivations, and then they launch a surprise attack on the Redcliffe leadership. Eventually, Fiona will succumb to manipulation that is more magical in nature. I actually just completed the War Table operation called The Serpent of Nevarra, which involved a Venatori agent using magic to cloud King Markus' judgment. We have, yet again, explicit evidence that the Venatori use magic to brainwash people.
This is my take on what happened as well.
I figure that the games timeline goes something along these lines, that in the first few days post-Conclave, the Templars present within the Hinterlands were gearing up for an attack on Redcliffe, thinking the mages were responsible (as most people did). With the formation of the Inquisition (roughly 6 or so days after the destruction of the Conclave), the Templars were recalled suddenly to Val Royeaux to answer this challenge, leaving only deserters behind to wage their own little private war against the Mages. With this temporary reprieve, Fiona learned of the Inquisition and decided to travel to Val Royeaux to attempt to meet with them, hoping to form an alliance and gain another source of protection from the Templars.
If Alexius had attempted to make contact with the Rebellion in this timeline, unfortunately, he waited too long until Fiona had other options available to her. Fearing that his master would be displeased to lose the mage army he wanted, Alexius decided to cheat and jump back to 2 days after the blast, at time when things looked most bleak for the Mage Rebellion.
Arriving at Redcliffe earlier this time around, Alexius was able to convince her that agreeing to his deal to join the Imperium was the only chance at salvation from the Templars. Around this time Alexius likely seized control of Redcliffe from the Arl, kicking him out of the town. With the formation of the Inquisition and the Templars being recalled to Val Royeaux, Fiona realised that she'd made a horrible mistake.
The timeline being something along these lines would explain a few lingering questions, such as;
Why Alexius needed to go back in time? - With the Inquisition to provide another option, he wasn't able to convince Fiona to join him.
Fiona's appearance in Val Royeaux? - She either rejected or delayed Alexius' offer, hoping for an alliance with the Inquisition.
The Rifts forming in Redcliffe post-VR? - The result of Alexius punching a hole through time and tossing it in the privy, to paraphrase Dorian.
The change in Fiona's demeanour? - Why she's so confident and self-assured in VR, but clearly miserable and stressed in Redcliffe.
At least, that's make take on it?