As for all seers dying in the annulment, that's simply not true. Remember that out of 15 circles, it was the only one the annulment succeeded. It failed in the other 14, do we assume every single Templar was killed in those? Because "failed annulment" seems very decisive in terms of who won and who died.
Didn't the Annulment at Dairsmuid take place before the breaking of the Nevarran Accord, since it's implied it was the only time it was called for between the Kirkwall rebellion and the outbreak of the Mage-Templar war?
I think part of the reason that it succeeded at Dairsmuid was because it came so unexpectedly and that the Circle was far smaller than most others, which took everyone by surprise and gave them little chance to man a decent defense.
During Ferelden and Kirkwall incidents, we saw a few dozen mages going on the offensive was often enough to take the Templars by surprise and force them to retreat, regroup and recover before they figured out how to deal with the threat.
For the Circles that fell during the war, it probably happened in a similar fashion, where the mages wanting freedom rose up and took the Templar garrison by surprise and by the time they realise what had happened, they'd already staged a mass prison break.