What I would do, is just simply have a pleasant chat; perhaps over coffee somewhere. Go wearing pants, but just ask her straight out what it is that bothers her about your kilt wearing. You two are good long-time friends so I think that she'd plainly tell you why. Tell her that you won't be offended by her answer, that you just want to understand. Once you find out why she is not comfortable with your kilt-wearing you can address it.

Thunderbolt mentioned that it is normal to men to wear kilts. I have to disagree. If kilt-wearing was normal you'd see more of them. In actuality, with your wearing a kilt, you're actually being odd/different/weird/strange. It has been over two years since I saw someone wearing a kilt that wasn't at a highland games or kilt night.

So I think the best idea is just to get it out in the open. Ask her why she doesn't like your kilt-wearing and once you have her response, just reply appropriately.