Having just sorted this out on my daughters sei I'd say the first thing is to check if the drain holes are actually blocked.
Pop the sunroof off (there are a couple of guides on here) it only takes a minute. You can then see the drain holes - one in each corner on the gutter. Pour a little bit of water into each corner and watch it drain away. If you do it on a dry day you will see the water run out from the sill area. A blockage will be immediately apparent as the water won't run down the drain hole. I gave a quick blast from an air line which cleared the drain then ran through some clean soapy water followed by a fresh water rinse. It only took me 20 minutes to cure the problem. If the air line doesn't clear the blockage then you can start thinking about folded sill edges. If you've only got one blockage you'll know whereabouts the drain holes are on the opposite side of the car.
If all the drain holes run clear you've only spent 5 minutes proving that the leak is somewhere else!