This is an extremely general question, kinda like "I just met a girl on the street, what should I have done".
However, in order to come up with some random suggestions:* Tell her "really nice to meet you, but hey, you really should be wearing pants or at least a skirt". After C&Fing about that for a while, tell her the story about when you went out for a short errand and only afterwards realized that you had forgotten to put on pants. You had even been talking to an acquaintance, and she seemed normal to you. DHV by explaining it by the fact that as long as you keep your posture and confidence (which you did, not knowing of your improper dressing) you can get away with anything.
* Tell her about how you just met someone who looked a lot like her and who acted like a complete idiot and follow it up with a funny story about what this person did. Then get her to qualify herself by asking her if she's like that too ("you obviously look like that kind of person") and ask her if she has any weird behaviors of her own.