I also have a 2006 Torrent, and in the last year have had the same problems. Most recently i got in my car after a long steady rain to find the same few inches of water pooled in the front wells.
I've done a lot of research and this is what i have found. The drain holes in the torrent sunroof are prone to plug up. Dirt and gunk build up quite quickly, and i've been told the only way to solve the problem is to make a regular practice of blowing them out to make sure there is a clear path for water/debris to travel. I've read it should be done at least twice a year...particularly in areas that see lots of rain or snow.
I'm afraid that if your vehicle isn't still under warranty - and i'll assume it isn't, there really isn't any recourse for you to pursue with the manufacturer.
Any honest independent mechanic will clean out these drain holes for a $50 or less...and once you have seen it done, you can probably do it yourself at the local gas-station using their forced air compressor. Your dealership was either gouging you on the price... or charging a rediculous sum to dry and clean your interior. I was once quoted $400 by a gm dealer to have my torrent "detailed"... i was disgusted.
My advice would be NOT to rely on duct tape. It's great in a pinch... but i don't know that i'd expect it to hold up beyond the first serious rain storm.