Time Machine: Can I back up different clients to different disks?
Yes - assuming you have OS X server running on the Mac Pro, you could share each drive under a different name and enable both for Time Machine backups.

You could then configure some portion of the machines to hit share A and the rest to hit share B. Since each computer stores backup contents in a sparse disk bundle, you could even shift a backup or two to the other drive and then reconfigure things if your initial allocation wasn't working after some time passes.