Because their front had completely collapsed.
Their gamble in the free marches failed, the island their dreadnoughts launched from was captured. All the progress they had made into inland thedas was pushed back into Rivain.
One fortress was left to them at the time of the armistice.
The Qunari stopped fighting because they were losing.
Is this true? Doesn't the codex mention that it wasn't the damage to their armada or the loss of their troops that caused their retreat but rather the deaths of the Rivaini population?
On a separate note I'm not a big fan of the Chantry but I would like to see more of the Chant in Inquisition. Maybe one day if there is enough fragments we could put it together as a book.