It's not possible to absolutely control the contents of the system disk. There are things that will help, though.
First, with a home-built server, start off with two disks. Windows Home Server will only store duplicate files on the system disk as long as there's room on the second disk. Then make sure that you always have at least as much free space as the size of the system disk. That should minimize the amount of data that Windows Home Server will be forced to store on the system disk.
Over in the developers forum you'll find discussion of a tool (unsupported, use at your own risk) that attempts to force data off a disk by filling that disk up with other data. Used on your system disk, it will tend to push everything else off.
But even with that, there's no guarantee that data will be excluded from the system disk, and no guarantee that doing so will protect your data any better. My recommendation, therefore, is that you not worry about it. Accept that the loss of your system disk, just like the loss of any disk, risks the loss of files that aren't in duplicated shares. This includes the backup database.
I'm not on the WHS team, I just post a lot. :)
