There is no proof they were brainwashed.
How does this make sense? This is a world wide conflict. How could the mage rebellion come to an end with the death of the mages in Redcliffe? Or is it that you are only disbanding the templar order in Ferelden?
The rebel mages in Redcliff are the bulk of the rebellion, withouth them, the rebels lose their forces.
You disband the entire Order, almost all templars joins the Inquisition, with the exception for the ones who didnt left the Chantry and the Hanshall templars who you can recruit via war table.
So then who will watch the mages?
If Lelliana is the Divine, no one.
If Cassandra or Vivienne is Divine, they reform the Templar Order.