Jack answered this. He said he didn't believe Jacob would want Desmond there unless he would be able to help him so he didn't believe MIB was right about Desmond being able to destroy the island. He had faith that whatever Desmond did down there, it was going to be necessary for them to come out on top (and it was).
Okay, so ultimately it was necessary for him to go down there to revert the MiB to mortal status. That's perfectly clear but they didn't know that so it was a lucky guess?
I apologize if I'm missing something obvious. I only got to watch it once and my girlfriend was trying to get caught up enough to understand what was going on.