Ah, I think this should be possible if you are using linux. ^//^ I haven't done it yet (thus my googling and stumbling upon this thread), but I know that with Vuze you can specify an interface to use for the connection. Bassically, since vpn's create virtual interfaces you shouldn't need to have a second physical connection.
If I'm not mistaken, you should be able to just configure OpenVPN or some other encrypted connection and then just change the routing table to bassically "break" openvpn in the sense that all your traffic won't be directed through it. After that, you should be able point vuze to use "tun0" or your distro appropriate encryption interface.
I'm looking to do this as I basically lost all of my music (300+ cd's worth) in a very complicated situation involving all of my things being put in a storage unit and then the people who owned the storage unit skipping the state and selling their tennants more valuable belongings.
I'm also in the same boat as you in the sense that I have several other services tied to a domain name need the bittorrent side of things to be separate (The idea is that I'm creating a private web host with all my music, movies and manga on it so that I can have access to it from anywhere I am on any computer I'd like.) I'll post what I find out based on what I am going to try. If it works I'll let you all know and probably post it in my very unused and crappy blog. ^^;;