The Mage Army that managed to fight one of the strongest fighting forces in Thedas, The Templars, to a standstill?
Just going to throw out that they never did that.
By the time of the Conclave, the only mage forces in open rebellion are the two mage groups in Western Ferelden: the Rebel Mages in Redcliffe, and the power-mad apostates right outside the gates. The former are hiding behind the protection of the Ferelden Crown even as their VIPs are negotiating in the Conclave, and the power-mad apostates are being matched by a rogue/renegade Templar element.
Everywhere else, the Templars won in the field- there are mages who've gone to ground, but it's the Templars who have garrisons and overran various circles and otherwise pushed down any and every prospect for a Magi free state.
By the time of the Conclave, the Mage Rebellion as a Mage-Templar conflict is effectively over and lost: the only 'advantage' the Mages have is that if the Templars attack Redcliffe, then Ferelden's Crown would be drawn into the war on their side, and Ferelden would beat the Templars.
The Conclave is really a high-stake game of chicken in which the mages had a strong hand to negotiate their own surrender. They'd already lost the war in terms of being able to determine their own fate: all that was really left was to negotiate the terms of their oversight between the Chantry and Templars and Ferelden's Crown.