Time Machine could be used in conjunction with the data already on the drive (it will leave it untouched) and you can keep the same Silverlight back-up strategy if you want. It will just cause it to fill the drive faster as TM will eventually use up all free space left available to it.
However, I would recommend getting one drive for the Silverlight back-up and another for Time Machine as redundancy of back-ups to two different drives would be more effective. As it is a Mac Pro, you would only need to get another internal drive rather than an external and dedicate it to TM backups, which would keep the price down.