Short answer. If you've got enough hard drive space, copy the contents of the DVD to your hard drive, run from there, profit.
I didn't have that much space, so I copied the setup.exe, and ran it, causing it to at least make the appropriate directories under Program Files. Then, I copied the piggs folder from the DVD to the "proper" place on the hard drive.
When it was done, I ran the patcher, which installed/mirrored al the files that were missing.
Believe it or not, my creaky P4 2.8ghz with 6800GT will run STO at the lowest settings, but I was still able to bump up the res from 1024x768 to 1280x1024.