A touch probe is probably 'always' going to leave some kind of marks or lines and yield a "textured" surface in the scan-model itself. I also have a probe for the ShopBot (actually two...one 1/16" tip and a 1/8" tip) and apparently they all work the same. I've seen some folks put little plastic balls on the tips and of course, some people use the glue tips to help minimize the "damage" to the article being scanned. (A laser scanner is the only real solution to the problem.) The sharper the probe tip, the greater the detail it picks up, but also the greater the "scratches".

For valuable items you want to probe-scan, never scan the object itself. Rather, you would make a mold, then a casting of that, then scan the casting instead of the original object. Smooth-On has everything you need for such a task: http://www.smooth-on.com/

I outlined sort of a cheap method of making a scannable item from something that normally could not be probe-scanned in a Tips & Tricks article. See page 4 of this article:

ISSUE 9 June 2008 – Scanning Probe Techniques