They told me that the rust was not bad enough to replace the entire doors since it was only on the railing and underneath. He told me there body shop was going to "blast" of the rust put down a primer, coat it with some kind of rubber sealant then put there weather stripping back in. I will inspect the job when its done. They did tell me though if they do start working on it and it looks really bad or didn't notice something the first time they saw it (when they inspected it and took pics) they will call me back with those 2 options as stated before.

If its anything I hate its rust on a fairly new car! Hell any car for that matter.
Its an '05 and I don't want to be driving around the Titanic!

I'll keep you guys posted and hopefully this turns out ok with no problems. And again Andrew thank you for that post. I think you may have saved my doors!