Jim, I like the idea of the Freedom of Choice race. I would have run the event the following year, mostly to see if the same guy lead again, and if he reversed the course for his second running.
But, as for the initial post, I think if the Race Director wants to pay for a second certification (at whatever cost you work out with them), why not issue another cert?
Jim's previous post has the second-best argument for certifying the reversed route - if the race advertises the cert number, as they especially should in this case, the runners will be able to really know the route, instead of being surprised by the reversed direction. (The best argument for certifying the reverse route is that the race director wants it, and is willing to pay for it. Don't get caught up in "it is needless paperwork", as that is a lazy excuse. If I want to certify the same course each year, and am willing to pay for it, I should be allowed to hire the job out every year.)
That said, I don't think a re-cert should be required.