Well, I had to find out about next year any way so I gave them a call.
Alaska Discovery does run it's own trips. At least to Pack Creek where I'll be going. She also mentioned Glacier Bay but I didn't ask if they run that one or not.
For those who are thinking of doing this independently, it is possible. The biggest hurdle would be getting a permit. Alaska Discovery does rent out kayaks by the day. There is a campground on Windfall Island run by the National Park (I believe) and there is a flight service that will take you over (I believe I read $250.00) but I'm not sure what the min. number of people ect. This will have to be researched. I know there is at least one trip review of people that have done it independently.
I'll be talking to them later this year in June for next year. $450.00 is a little steep just to go over for 4 hours. You can spend roughly 1/2 that and get 2 days out of it.