Well, your goals do need to change in accordance with changing circumstances.
Plus, when they rebelled the circles offered neither freedom or security.
So their goals changed from freedom to survival....and even going with that idea doesn't really work. They will be forced to fight the Qunari or other tervinter enemies for a peroid of ten years, and be treated as nothing more then slaves. No matter how you try and spin the decision to side with Tervinter it isn't to the benefit of the mages. Alexius even hints that ALL mages even the children will be used as fodder for war.
It was a stupid decision, their best option would to have been to stand with Arl Teegan, his men and boot Tervinter out of Redcliffe. Then the Arl and Fereldan Monarchy might have felt some gratitude for helping repel a foriegn power.
Fiona betrayed the whole idea of the mage rebellion in the first place, FREEDOM, for indentured slavery. She bascially traded one jailor, the chantry, for another, tervinter. And the mages are worse off for it. To the common peasant she proves everything they fear about mages to be true, "Give mages freedom, and they turn out just like tervinter." Now granted that isn't quite true but the common peasant will only see mages joining tervinter, not that mages are nothing more then slaves with magical ability.