The
Cult Membership Card (and to be clear, the one from
Munchkin Cthulhu, not the Promo of the same name) allows you to choose whether you want to be a Cultist for
each thing that would affect them individually.
So in your situation, the player with the Cult Membership card would probably choose not to be a Cultist for the purposes of ending the game, and they would also go up a level for being the last non-Cultist. They can even keep their Cultist-only Items in use while claiming this. If the card carrying member ever did have the highest Level, they could choose to instantly end the game and win too.