My dd is in the 94th percentile on BMI like your dd (my online calculator said 94th, not 97th) -- "at risk of being overweight". She's in the 94th percentile for weight and the 84th for height.
The thing is, that dd has had these SAME percentages since she was an infant. Her doctor (who isn't holistic at all, but very practical, and I love her), said "well, this has been her growth curve all her life. If we see the weight and the height percentiles starting to diverge, then we need to be a little concerned." Honestly, dd came out built like a linebacker. She was OVER the 97th percentile at birth, and about the 95th for height at birth. She's got beautiful broad shoulders and a lovely little hour glass figure (from her dad's side of the family). The women in my family are chesty with broad shoulders. As one of my friends put it, "She really does look like German peasant farmer, doesn't she?" She's strong as an ox and has a fair amount of muscle and a little fat. She's never going to be a size 0 or a size 2. It's not in her genes. When she's grown and at a healthy weight, she'll be a size 10 or 12. (That's what my mom and my sisters who are at a healthy weight are.)
Dd is 4' 3 1/2" tall, and weighs 73 pounds. Her brother is 4' 10 1/2" tall and weighs 72 lbs. He's always at risk of being underweight. The thing is, if you look at their diets, dd's is probably more healthy than ds'. For her snacks, she chooses yogurt (low fat), turkey, ham, and fruit). She gravitates toward protein. Ds's pants stay up, as far as I can tell, because of the copious amounts of Nutella that he eats. He is much more likely to tend toward carbs. He stays lean because he moves constantly.
Dd is, probably, at risk for being overweight, but that's largely because she's more sedentary, and has decided that she doesn't want to do any sports where she has to "run and get hot". So, we've enrolled her in swimming. We're reducing the amount of TV she watches (it got a bit excessive at the end of the summer because I was ill). But her favorite things are to read and play imaginary play with stuffed animals (where she does things like do homework with her stuffed animals!). Her brother's favorite things are basketball and soccer. Even in the living room, he does soccer kicks with a balloon. Dd reads.
I think your doctor is concerned because her weight jumped up fairly high in the last year, but her height hasn't. But all that says to me is: Watch out for the growth spurt! If she's fairly active, can do what she wants without getting winded, and you think her diet is well balanced, I'd relax.