I don't think she was right, at then end of the day, it's not like you're hurting anybody by wearing eyeliner. But like Kip said, no doubt she's just worried, doing anything different can either get you in trouble, or lead you into the wrong crowd. If I were you I'd just sit her down later and tell her she has no need to worry, you won't get hurt because of it, and that this doesn't mean you're getting involved with the wrong crowd or anything, you're just trying something out for fun. If she understands that, she'll be fine with it.
I have to say though, I find it odd that she's willing for you to miss a day of school over this. :?