Your BES 3.6 server can be a Windows 2003 box "independent of your Exchange Organization Version" your not running Exchange Server on your BES server.... however, there are a few things to look out for.
1. You will need to load Exchange System Manager 2003 instead of the Exchange 5.5 Admin Tool (this also requires IIS to be loaded ... WWW/NNTP/SMTP) ... you can disable all of them after you get ESM 2003 installed)
2. You will need MSDE 2000 ... make sure you also apply SP3 to plug the security holes
3. Apply the most recent CDO.DLL (see the CDO matrix in the install guide for 2000/2003) .. it has a matrix of what CDO you need for a given OS.
Now my AD Domain Controllers were already at 2003 before I put my BES servers on 2003 .... I dont know if you can have a 2003 memeber server in a AD that has only Windows 2000 domain controllers ... I suspect not.