My first stop would be the dermatologist. They will be able to tell you what is safe to use on her young skin, and what will work well. I don't think I would use anything that is made for adults or that you get at a drugstore. Even though I use regular makeup myself, there are a lot of harmful chemicals in makeup that I would not want to put on my pre-pubescent daughter, because they can affect their hormones. So I would be very careful there, even of the so-called "natural" products, some of which were listed below. They are not very natural when you check the labels. Like I said, I do use them myself, I just would be more careful for my child since they are still young and growing. You can check this website too www.cosmeticsdatabase.com and it gives a lot of info about the safety of individual beauty products, you just look them up by type or name. But to get an idea of one that is safe and will work well, I would go to the dermatologist.
I also agree that you should maybe let her talk to a therapist, or maybe just consult with one yourself on the best way to get her comfortable with this. I am not saying you shouldn't let her cover it up, I would probably make that same choice, and I know you didn't come by it lightly. But the probability of keeping it covered constantly every day, all day is pretty slim for a young active child, so there is probably going to be a day soon enough that a classmate sees it. And if is has been covered to that point it might be even more noticeable to the other kids and get more attention. I would want to have some coping skills for her in advance of that happening. I hope she makes a smooth, happy transition into school, I know that this is scary for all of you. Good luck!