Doesn't seem off to me. What are the templars but the military arm of the Chantry, who are trained for the purpose of either hunting down and killing apostates, or policing them in the Circle? It is not a relationship of equals. Very few templars would be broken up about purging the circle, especially given what happened, with the mess being started by Circle Mages to begin with.
According to the codex, annulments are relatively frequent occurances, happening on average every 40 years, which is about once a generation, nearly.