To me, it doesn't sound like your boss was rejecting it - it sounds more like the question caught her off guard and that SHE's concerned that having one of her employees show up kilted might get her in hot water for allowing it. There's a huge difference between "I'm not sure that's appropriate" and "that wouldn't be appropriate".
I doubt she'll do the research on the topic on her own, so (much like piperdbh suggested) I would recommend you put together a little presentation (on your own time, of course) that you could give to her on why you want to wear a kilt with pictures of what you would look like if you did. This could be a PowerPoint that you email to her, or something you actually show in person.
After bringing the point up, I would not simply arrive at work wearing a kilt - that is just asking for trouble that you sound like you don't want.

The beauty of a presentation with pictures and explanation (and maybe a copy of the company dress code and how a kilt fits it) is that she can pass it on to her superiors if need be and ensure that she's not going to be accused of neglecting her managerial duties.