It shouldn't take them that long to drill out the 6 bolts with proper tools. Your getting a new fly wheel anyways so they can do what ever they want to remove the clutch plate. You should be worried if they mention that the Flywheel bolts holding it to the crank is stripped. Also if they are charging more than you can afford bargain with them to provide your own OEM clutch kit. It is alot cheaper to purchase it outside of the dealer for a Exedy Clutch Kit ( Almost half of the price ). I did this when my car went in for tranny problems but the clutch was not covered under warranty and they didn't want to put a new tranny in with an old clutch. So I provided the clutch kit ( $175 vs. Dealer $600 )

As for going somewhere else, your prety much held hostage cause they already removed the tranny and will charge you to put it back on.