jascal...assuming there are no blisters and you haven't lost the prop shaft to electrolysis, there is no reason that leaving the boat in the water itself should be of major concern. If on survey, the hull appears saturated with water it can be dried and barrier coats applied before bottom painting.
I suspect that your major headache will be the barnacles on the botom if the bottom
paint has lost its' effectiveness. The removal of all remnants of them is labor intensive as you don't want to strip the gel goat along with the critters! Good luck!