Okay, first off the missionaries deserve everything they get and I have no sympathy for them if they're eaten *BG*
I'm not sure what the constraints are. I presume someone is always needed to return the boat to the opposite side, and that can be either a cannibal or a missionary, or is it just missionaries that can handle the boat? Are they safe while they're in the boat (i.e. they can just drop one person off)?

Does this work? cccmmm(3 of each on one side)
cm go off in canoe leaving ccmm
c deposited on opposite bank, m returns to ccmm
cm go back to other side (to c) leaving cmm
c drops off m and returns. One side now has cm, other has cmm and c is in the boat
m gets in, crosses over with c,
now one side has ccmm, other side has cm c crosses over (leaving cmm) and picks up m now there's ccmmm on one side and c on other so either a c or an m can go and pick them up.

Something tells me there's an evil constraint I haven't considered.