If you destroy the Cult faction, the cult do will still spread, then your cultists may commit mass suicide.

If you don't want to take the risk losing too much people, you have to endure the cult: When half your community is converted to the cult, some may suicide.
Then only you will be able to officially ban the cult. It will stop suicides and very slowly the cultists will abandon their fate.
Dahlia sisters may help you, but only as at least a quarter of your community is still in the belief.

EDIT: Here I mean the ChosenOnes cult, the faction appearing middle of the game,
I didn't mean the survivors prefering drinking water in church than praying SaintPatrick in bars :)

Or - remove all churches in your fort. Isolate all cultists. With time they will lose their cultist perk. (Same as people who are devout will stop being devout after some time if there are no churches in your fort).