I don't pretend to know much about rules and regulations for trail races and other off-road events, as I am mostly a road runner, but the few local trail races I'm involved in seem to allow any sort of footwear one deems appropriate, even to the point where I saw a guy set out to run a tough 50-miler on technical trails in Crocs (he didn't finish). It would seem that races w/rules regarding footwear are in the minority and would be easily avoided if one didn't choose to comply w/those rules. Now, I'm in the US and the event you're talking about is in Scotland, so perhaps things are different, but it seems to me there must be other races that DON'T have this footwear rule. I would have to agree with pace2race that you have voiced your complaint to the appropriate folks at this particular race and, for this year at least, the answer is no. They do have that right, like it or not. In your shoes (or out of them!), I would simply set my sights on a different race.
It seems that your statement regarding how "you can't race in shoes that work" = "you can't race anywhere ever" might be a little overstated, as I have to imagine there are any number of other races that allow you total freedom of choice regarding footwear or the lack of it. I have seen barefooters in virtually every local road race I have run in recent years as well as while running non-local events like Boston and the Twin Cities Marathon. Boycott races that don't allow Vibrams/barefoot! Voice your opinion to the organizers clearly, intelligently and respectfully and do not participate. You may miss your chance to run this particular race this particular year, but disappointments happen to runners all the time--an injury prevents training well or prevents one from even racing, bad weather rules out a good performance, illness affects the outcome, and so on. Write it off as something that just won't happen this time around and move on to the next goal.
Best wishes in the future!