Well, if you did understand it right the first time, I sure didn't catch up on that. As you said, the Russian literal translation doesn't really convey the same message and I totally agree with you. Будет ли когда-нибудь конец sounds like you really want that to end already, while Конца никогда не будет? sounds as if you're very suprised at the fact or that's your very irritated with that.

So I say you have to forgo the literal translation and come up with something like:

Закончится ли всё на этом? Неужели это (ещё не) конец? and such.