Cassandra lets the mages run the Circle themselves, no? Honestly, I think Cassandra is the weakest of all three candidates. It seems like she's not very decisive with either faction, which is something I would not expect from her.
"Let the mages watch themselves...with our help." What means is anyone's guess.
Depending on the status of mages and Templars, the mages can form the College but she still restores the Circle and they end up clashing or they just join the Circle under Cassandra.
The Templars can rejoin the Circle but without a leash or join the newly formed Seekers or just join the Templar Order under Cassandra (which happens if Cullen is convinced to continue taking Lyrium)
Her ending appears to be a middle ground between Leliana and Vivienne and possibly the closest there is to a return to the status quo for there is always a Circle and a Templar Order. But we just don't know how it all works in practice.
I really with the Inquisitor could have sat down with the Divine and the leader of whoever we sided with and try to figure out how it would all work.