I've thought of having the Southerners simply leaving, but the players have shown a lot of interest in ending them. Plus, I can always bring some other mutants back later.
Excellent! That gives them a motivation to follow the mutants when they leave. Unless the Southerners are incredibly dim-witted, you'd be doing them a disservice if they stayed where they were and waited for the heroes to come slay them.

If I may leave a suggestion: leave the players a note when they come back.

To Whom it May Concern:
We heartily congratulate you on your successes in stalling our plans, but wish to inform you that your efforts have been for naught. We would like to invite you to the grand Cathedral in the Whispering Wind Cavern so that you may be present for the end of our works.
Signed,
The Grand Cleric of the Southern Religion.

The cultists don't actually have anything in that cavern, and it is purely a trap for the players. Have it inhabited by an ill-tempered dragon or full of slimes that want to dissolve their meaty bits. That way, the players can go slay some completely unrelated beast and become irate when they learn that they were played like chumps by the Southerners. Nothing is better than having an enemy that is HATED by the players.