She does protest him changing the terms of the deal, though. "You said my people wouldn't be military. There are children and those not suited." Yes, she does still follow him at the end of the scene, but she doesn't look happy about it. In the hall in Redcliffe she also yells out, "You can't involve my people in this!" after Alexius explains about the Elder One and his grand ambition.
She puts up a heck of a weak resistance.
"No! You can't!"
"Yes I can!"
"Oh, right then. Back to the castle?"

I'm judging her based on her actions, not her words.
If she was really committed to not having her people being used as front line forces, I think she would have protested attacking Haven and most likely either been killed or imprisoned by the Venatori. And yet...
Fiona and most people think Teagan left by himself, actually maybe he did. He didn't know Alexius was with Venatori of course, but I don't think he could stomach a Tevinter Magister in Redcliff. Whether Alexius forced him out or he left by himself, everyone think he left by himself. So in the end its not an issue that should take priority over safety of mages with Children among them. The fate of the Tranquil is sad but if you paid attention no one noticed what happened to them except the other Tranquil. Tranquil followed mages because they had no where else to go but they were not in any immediate danger like other mages so while sad no one in Thedas is looking out for them, or cares what happens to them. At the time anyway with the war and torn open veil.
The fact remains that if Alexius was not with Venatori that deal was the only option that would protect the mages. By the time Inquisition reaches Redcliff is when Fiona is starting to doubt something is wrong, and objects to Alexiys many times. (I was going to post the lines but while I was writing this post nightscrawl posted right before me so read the above post). Fiona and the mages fight to the bitter end after Inquisitor is sent into the future, with Fiona as sole survivor. So they end up completely throwing the deal out of the window once its revealed Alexius is not speaking for Tevinter but Venatori.
The game states that Teagan was kicked out. And if Fiona didn't know this, then she was willfully burying her head in the sand. She is still nominally the leader of the mages under Alexius' protection, she should not just abandon all sense of responsibility and allow the Tevinters (Venatori or not) to ignore Fereldan law.
So fate of the tranquil:
Tranquil Clement: "All of my fellow tranquil are mysteriously disappearing. Would someone please investigate?"
All other mages: "Shut it, we don't want to learn enough to be an accessory to murder!"
like...the mages were all hunky dory with tranquil disappearing? Tranquil wouldn't just abandon their post for no reason like a scared refugee might. Remember the tranquil in the Ferelden Circle who stayed at his post despite abominations everywhere? Anyone used to tranquil must have intentionally not thought about why they all started disappearing at the same time that Alexius came to town. Conveniently right after the Conclave exploded.
And it's not fact that if Alexius wasn't Venatori he would be the only option for the mages. Ferelden was already harboring them in a castle and showed no sign of kicking them out. They had offered shelter before Alexius ever showed up. Fiona chose to abandon that offer in favor of Alexius.