Transmission 0.70 just came out. You can grab it here.
For those that don't know, Transmission is a BitTorrent client. Why am I pointing this out? Because it has a new feature where you can keep complete and incomplete downloads separate. What this means is that you can use it with Hazel without Hazel moving files before they are done.
I haven't had time to play with it much but it seems that what you need to do is to make sure incomplete downloads are stored in a different folder. Point Hazel at the folder where (complete) Downloads are kept and you should be good to go.
Report any success or failures with this here if you get a chance.
Enjoy.