Bride and Groom can invite who they like. Their say is final.
But, as a Bride to be, I as think a Grandparent, you do have a place to ask - (not demand to be clear!). Certainly if mine were to ask if someone was invited or otherwise, I would explain - not exactly justify or change - but at least pay heed.
Asking her to be flower girl is a little much! A - she's more a young bridesmaid, and B - that's not to say other closer-to-the-bride girls were passed up due to it being childfree
Are other cousins invited, and is this girl excluded only by virtue of her age - if so, it could be worth approaching from that angle - as in a bit unfair to exclude only one of your cousins.
If other cousins are not invited - fair enough, she shouldn't be invited just because she's the sole girl.
For comparison, I am generally not inviting cousins to the wedding itself - but I have mostly adult cousins. But the exception being 2 child cousins - because they will need to arrive with their parents and couldn't arrive just for the evening reception alone.