They don't have to kill all the Wraith and they wouldn't. They would only kill those that would continue to attack them. Once peace has been reached I'm sure Atlantis would stop having to defend itself.I was really upset with how the 'heroes' discussed committing Genocide in this episode. It was bad enough when Sheppard (and of cause Ronan) wanted to blow up the hive ship at the beginning and murder the defenceless wraith on board even though they'd come seeking help. But contemplating 'getting rid of the wraith once and for all' aka genocide and the only argument against it was that it might not work? Atlantis has always had questionable ethics but this went too far.
Charlie
The remaining Wraith would be happy to co-exist with the rest of the people in the galaxy.
You do know that if the treatment dosen't work the Wraith have to feed off oh humans to survive don't you.
Then the part about "They would only kill those that would continue to attack them" would apply again. You did realize that didn't you?