Interesting question, and one we've talked about in PortLUG. Minifigs have been handled differently in each of the few drafts that I've participated in, but in general, it seems that the general rule is that they're kept together. Personally, I don't really care one way or the other. The first time was with 5982
Smash n Grab, which has both an alien and a police minifig, and the general consensus was for everyone to keep their own minifig. The next was with 7197
Venice Canal Chase, and IIRC, everyone kept their own Indy and Elsa, but the two guards were in lots, and I think the fezzes might have even been another lot. And finally, we drafted three 7573
Battle of Alamuts between some 6-8 people, and so since the minifigs didn't match up to the drafters, each character made its own lot, to be chosen in a second round of the draft that was only including the minifigs.