A: No. The idea is that the Secret Cultist benefits from the end of the world in ways regular players do not, so everything is backwards – that which would normally make you lose now helps you win. So if victory is found through the Minions of Darkness, it’s just a bonus if Cthulhu himself also joins the party!
While the win conditions for the (non-secret) Cultist are more narrow, the same is true, since they’re winning with an UnGoal, reveling in the destruction of all we hold sane.
This situation also happens in a game of Zombie Fluxx if the Zombie Boss wins… but there’s little question about whether Zombies would prevent the Zombie Boss from winning. On the contrary, they presence of a ton of Zombies is exactly what makes the Boss win.