You can vote for whichever mission you want, of course you can always try to converse and figure out which one might be the wisest decision. As for intelligence, I think it should be said now that you vote intelligence options separately by number..

For example:
"I vote on Jailbreak and intelligence option 3."

Then, even if Jailbreak wasn't the final vote, you still have your vote in for option 3. If intel option 3 wins the vote, then whichever mission is chosen will have option 3 unlocked. It might look something like this...

Door to Door: 2
Jailbreak: 1
Underworld: 1
Wait: 0

Intelligence Option 1: 0
Intelligence Option 2: 2
Intelligence Option 3: 1
None: 1

Door to Door has been selected as the current mission.
 - Intelligence option 2 unlocked (-15 Intelligence).

I hope that makes sense. I will add intelligence votes to the operations tab now.

EDIT: [hider=Changelog Update]
[b]9/6/2016[/b]
- Intelligence options have been added to the 'Votes' section of the 'Operations' tab.
- Votes for Mitra Chapter 1 have started.
[/hider]