I've seen floor pans way worse than that. You'll be alright. Get as much of the rust off as you can, clean it with something like alcohol or acetone, and coat it with POR-15.
You can then topcoat it if you want but I didn't bother. I used POR-15 on my floor pans over 10 years ago. Still going strong. I filled some small holes by using JB weld and the head of a nail. Grind off the rest of the nail after the JB weld hardens. If you have access to a quality welder that would be a superior option.