Wow, that's a tough one. If he's the independent sort who isn't easily swayed by peer pressure, I'd say go for it. If not, then you'll definitely want to make sure you talk to him at great length about it and make sure he really understands the potential consequences.

It may help if you "talk it up" with the other parents so they know in advance that he's going to wear a kilt so that it reduces the shock value at the ceremony. Plus, getting the word "kilt" out there with the other parents minimizes the chance that their ignorance could cause confusion over a boy wearing a "skirt".