Depends on kind of encryption you have in mind, but generally speaking this is waste of time/space/money/whatever.
1. eMule don't support it, server don't support it.
2. Encrypting data will not help you, 'cause you trying to hide header, not data.
3. Encrypting header is not possible, 'cause we need to exchange keys somehow.
Theoretically speaking we
may come out with some scrambling scheme for packet headers, to make matching in router impossible, but (1) and (2) don't make it possible.
so if they find a P2P packet then they just won't let it reach its destination
I don't know what kind of contract you have with you ISP, but if they simply drop all ed2k packets - in my country that would be simply illegal. I suggest you use low-tech methods i.e. call them and threat by legal actions.