I have experimented with this and found that I got blobs instead of sharp Stars with IS on.

I had a Canon 7D with an EF 35mm f/2 IS Lens, mounted on top of an Equatorial Mount on top of the actual Telescope. Both the “Right Ascension” and the “Declination” Axis’ were each driven with their own Motorised Clock drives in sync with the motion of the sky. The exposures ranged from 2 minutes to 1 hour.

The Images with the IS off, were sharper then they were with the IS on, which often resulted in blobs.

Therefore, I would suggest to keep all stabilisation off when on a tripod; Tracking or not. Your thought process may be the same as mine where you may be thinking that as the stars are moving very slowly, image stabilisation will help to keep them sharp for a longer period of time.

But that is not what happened with my experiment.

if you keep the IS on, you risk creating a "Feedback loop" or sometimes known as, “Shake Return", where the camera’s Gyros detect the continued IS Vibrations and starts to move around to correct this and as a result, you end up with a blurry image.

The best results I have found, have come from very Wide Angle lenses, such as the Canon 10-22mm Non IS EF-S Lens.