My 09 has plastic pieces that cover the holes where the roof rack goes. You should be able to get the pieces from GM. They shouldn't cost too much, or at least I hope they wouldn't .
I'd like to remove my rack as well. I actually had GM install it when I bought the car, because Yakima was saying the factory rack had to be on the car to attach my kayak rack. Now Yakima has changed their fit and you must puchase towers and clips....and the factory rack will get in the way.The rack covers the bolt holes that were apparent prior to it being installed, but I see no way to access those. I'm guessing you need to pry off the trim somewhere on the rack to gain access to those mounting points. Does anyone have a diagram that shows how to install or remove?
I took the rack off my 2009 a few days ago...The end caps of the rack come off quite easily. Push a flat bladed screwdriver under the front edge and work backwards. There's a small clip in there that will disengage. You can then wiggle the cap and the entire piece will come off. This exposes the bolts.Remove two bolts on each side (a total of 8 bolts to hold both rails on) and the rails are off.Now, I had saved back the small plastic covers for the attachment points when I had the rack installed. Unfortunatley, there was nothing to clip these to! Turns out there is another part, which was taken out and discarded when my rack was installed. That is part# 19184014, a small metal clip that bolts into the opening, and then the covers snap onto it. These were $7/each from the dealer. If you have the rack installed by them, make sure they save these and the covers for you, should you ever want to remove the rack.
Yes, why?? The dealer had none when I bought my Vibe and wanted $600 (ouch) just to order them in (Go find yourself a bridge and take a long leap I said...), the salesman and I both agreed that that was too much! Toyota wanted $300 for their version of Matrix roof racks (still too much).
Sorry that I can't answer your question, but I may be interested in buying your rack once you remove it. My Vibe did not come with factory racks and Pontiac does not offer them as an accessory.