I ran into this same issue on my last trip into the Q.  We ended up with 5 people when a group member pulled out at the last minute. When deciding between the options of 3 canoes or 2 canoes, these thoughts came into play:            
1) We had a couple newbies, so inexperience in the stern would have been a factor.  We had 2 members of the group that were the most capable.
2) We thought taking only 2 canoes might allow us to carry everything in one trip across portages.
3) We didn't think anyone would be able to keep up solo.
3) No one wanted to sit ackwardly on the canoe bottom for 7 hours at a clip with a canoe bar in their back.

We ended up taking 2 canoes, and we managed every portage with 1 trip across (a huge plus  :)).  The same 2 paddlers manned the sterns the entire trip, while the remaining 3 switched off equal time between the bows and the middle of 3 person canoe.  It turned out fine, and we said we were glad having done it that way.  The only downfall was trying to fish 3 people out of a canoe after we found that deep water walleye hot spot, but we were able to pull it off.  At one time we actually had a lake trout and 2 walleyes on the 3 lines at the same time.  Pandemonium in a canoe.