N.W.
I would wax it at a professional salon if it really bothers you. The hot wax doesn't hurt, and it really takes 1 second and it's over.
That being said, I think your child will be fine with one eyebrow. My stepdaughter has one eyebrow and the hair inbetween her eyes is quite light so it's not noticeable. She also has hair on her legs (she is 7) and I think letting her be natural is fine! (until she reaches the age where she chooses her hair removal)