I think 12 is a reasonable age to start on some make-up, especially if she is wanting it. And you've already taken that first very important step - skin care. If she gets in the habit of taking good care of her skin, she will look good with no makeup, a little, or a glamed-out dramatic look (for those special occasions as she gets older). Make sure that she washes both morning and night, uses a good toner/freshner (or a gentle astringent if she is acne prone) and uses an oil-free freshner.
For makeup right now, I would go with neutral eye colors (browns, pinks, maybe subtle purple or green depending on her eye color), maybe a very neutral cheek color, and mascara and lipgloss (make sure to get a good quality mascara!). A good foundation can also help protect her skin and even out tone, without covering freckles or making her look washed out - look for one that is labeled non-comodogenic!!
You may want to meet with a consultant who can give her specific tips on application and skin care specific for her needs. I know that Mary Kay offers free consultations as well as high quality products at reasonable prices - some other places may also do free consultations. Contact me if you're in the Salt Lake area (just click on my name) and I can set you and her up for one (I'm a consultant).
Let her have some fun with it - she'll want to experiment, let her when she's not going to school or church or something. In a few years she'll settle into a look, hopefully one you approve of :)