I had the same issue when using my Outback at a lake cottage. I have a floating dock, so I ordered two Suspenz Expansion posts and mounted/bolted them directly to the side of the dock, then I bolted two of their Big EZ Rack arms to the post, about 6-8 inches above the waterline.
http://www.suspenzkayakstorage.com/racks_pricing I use a couple of tie down handle straps attached together on one of the Outback's handles to easily turn and lift the Outback on its side while I slide it on and off the rack, directly into or out of the water. Then I purchased a Danuu Kayak Cover and attach it over the kayak.
http://www.austinkayak.com/products/673 ... 25-ft.html It's very fitted, so goes on easily, stays on and has held up great. 303 Protectant it good, but using a cover with it is best. Anyway, this system has worked great for me for the last 8 months or so, and isn't that expensive. It minimizes my time on and back off the water, which encourages more usage versus if I had to remove the boat each time. I left my kayak on the rack over the winter (because I actually kayak during the winter too,) and didn't see any ill effects, so would think if you cover it when you store it, it should be fine, but I would defer to Hobie on that question. Good luck, and happy kayaking!