Now it makes sense. All the backup options are volume based rather than file + folder unless you have R2.
I'm not real happy with windows backup either, having learned the hard way that system state can't be backed up to a network share - fortunately I had some extra drives lying around from some servers we virtualized. I never intend to use windows backup as a primary backup methodology, but it's nice to have in a pinch to help prevent RGEs when troubleshooting other problems. Thankfully MS has returned the ability to backup Exchange 2007 on server 2008.
I have been mostly happy with the Exchange integration in the new HP Data Protector 6.1, but HP DP is probably overkill for you. Perhaps something light like
BackupAssist might do the trick. They have a free trial and maybe someone else here has some experiences they are willing to share