1.Create a temporary subforum for the mafia to communicate in. Other mods should not be given access.

2.Lock the thread during the night (Zombo you didn't mention that the Townies couldn't talk during the night...)

3.Restrict thread access to currently living members.

1. They can communicate using e-mails or IM, I don't mind.
2. That was already planned.
3. Complicated, requires to move everybody to the same group, which takes them out of their current group. We will moderate the thread very closely to make sure no one else posts.

I'm just wondering...how the heck do the townspeople win?
It seems to me that the mafia is set up to win. They kill someone each night, and can talk outside of the game thread. I guess someone could really screw up and say "you PMed me this..."
Aside from that, how can the good guys win?

they have the majority. Yes if they sit around and do nothing, they will get killed,

The majority gives them a "buffer" to use. They can "afford" to sacrifice a few townies, if it allows them to gather extra information. If this information allows them to basically trade 1 good lynch for 1 nightkill, they will almost certainly win.