"I don't think there's any way Kyubey would just go away by himself.." Especially since he's apparently been doing it for so long on Earth already. Even if Walpurgisnacht wouldn't be threatening the entire planet, Kyubey would just continue his terrible magical girl practices until way in the future, Madoka knows it.

"That's why I'm going to wish for all witches to no longer exist. That way he can't make new magical girls either. It's the one way to solve everything.."

The whole problem with Kyubey, the whole problem with Walpurgisnacht, the problem with all the suffering her friends have gone through - all of it will just be gone, Madoka hopes. If her wish works out the way she hopes it will.