Didn't the betrayal was for conquering Doma and not his destruction ?
Spoiler Ninja storyline :
Because the ninja master comes to track him down without saying anything about destructing, Doma, he only speaks of heavy represions after the end of the war, which are obvious considering how the empire handle his conquests. It seems that he comes to track the traitor before 2.2, if not it might have been weird to send Ninjas track a traitor while they are trying to escape from the empire killing every domian around, moreover the traitor had enough time to greatly train a lot of ninjas for the empire and it must have taken a while between the betrayal and the NIN storyline.
But these ninjas don't come from Doma directly ( they aren't the same as Yugiri's ) but come from a secret village close to Doma so maybe the master doesn't know what happened very clearly.