I thought I'd seen it all. I'm pleased to see that you are raising a concern. For the life of me, I can't see why any teacher would have seen this as a good idea. Everything about it is wrong.
As others have said, it is very encouraging to give awards/rewards to children who come out top in this or that activity, who have shown the most improvement, who have put in the most effort, etc. It should be an award that has meaning and value for all children (so all will want to aspire to it, or something similar.)
Conditioning to conform to gender stereotypes starts at birth. Boys are "meant" to be active, competitive, "do" things, be independent, be assertive. Girls are "meant" to be well-mannered, attractive, helpful and passive. There are STRONG prohibitions against boys appearing like or doing things associated with girls. The underlying message is "girl things" are beneath them, inferior, second class. Yes, many parents try hard to counter this, but it's nigh on impossible to eliminate all the messages children get pelted with.
So, if girls that achieve something get certificates that are "girly" looking, they and the boys will already have some awareness that the award isn't as real, isn't as important to an award that contains imagery associated with boys, or is gender neutral. So the "lesson" here is basically, "Girls, no matter how hard you work or how much you achieve, it will never be as important or as valuable as what boys do." They're expected to be content as little passive "star princesses."
Surely, surely it would be better to give no awards at all, no recognition at all to any of the children rather than giving ones that further cement harmful gender stereotypes.
Explain clearly that you believe their practice is HARMFUL to children, in the same way that giving certificates with distinctive disabled and not disabled images, or different certificates with images of poor children and rich children to kids from different socio-economic backgrounds would likewise be harmful. Insist that they give awards that show value all children will recognise and aspire to, or ditch the idea alltogether. Even if they just didn't give awards to your child, she and all the other children would still see the same practice carrying on (and she'd also feel excluded if she was no longer eligible even for a really duff award.) I think you mentioned you were on Governors. If you don't get the answer you want, kick up the most almighty stink you can that way.
I know some people are a bit "meh" about whether separating kids strictly into pink and blue streams is harmful, but I suspect even most of them would find what this school is doing to be pretty appalling. Local paper interested in the story?