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It's a matter of personal preference. I don't think that a mix of skirt lengths looks awful, but I.m not a fan of it. But it's not like I'd be saying, "Ewww, how ugly!" at someone else's wedding. It's more like, I wouldn't pick pink BM dresses but I don't think it's bad if other people have their BMs in pink.
If you already told them that they're free to pick any skirt length they want, then I wouldn't change that promise now. It'll be fine, don't worry about it. The photos will look best if everyone is clearly happy and comfortable with what she's wearing.