Like I said, the descriptions of the contraction vectors for disease are... lacking. And limited. Especially since everyone seems bound and determine to play by the absolute letter of the rules rather than just playing the damn game and using common sense on those occasions when it warrants it. *sigh*
Anyway, for past Missions, my suggestion is don't worry about it. Unless a player goes out of his way to deliberately get the disease, have them get checked by a street doc at the end of the run and say "Wow, you got lucky! You're not infected!"
If they do go out of their way... Let them contract the disease, and then take away their character sheet. They just became a disallowed character type, and thus became an NPC. If that character is playing in the Seattle Missions, drop me a line. Maybe I'll put their Ghoul version in a future run as an NPC, for shits and giggles.
For Season 4 and onward, if we do put in anything like ghouls or bandersnatch that have HMHVV II or III, characters that can spread the infection through "contact", we'll be sure to cover the situation. Both of these are particularly dangerous and nasty, and could very easily be a game wrecker, so we'll tread very carefully, spell out guidelines for how GMs should handle it (If at all, it may end up simply be a case of "Hey, you got lucky!" to make life easier), and probably provide ways for players to resist the effects so that we're not just killing players out of the campaign for no good god-damn reason.
That said, we may use HMHVV I critters on occasion. These have the Infection critter power, and only Infect deliberately, rather than incidentally. Which means that we can use them to beat up PCs without fear of killing them via biological weapons of mass destruction (i.e., I don't plan to ever have Vampires deliberately trying to infect players.)
Bull