Firstly, congratulations! 
YANBU to put pictures of your wedding up, this is if you have the permission of the photographer as he holds the copyright.
YABU for putting them up before cropping or blurring after the mother has specifically told you she does not want pictures of her child on the net. I realise that there might be a lot of pictures, but she has already told you her wishes and as the mother of the child, they should be respected. It doesn't matter at they haven't been tagged, she has specifically told you that she doesn't want pictures of her child online.
Take them down and meet her halfway, especially if there are a lot to them. There are some very secure websites that allow for photo sharing with a specific email invite and password. Ask her if it would be acceptable to out some on there, pointing out that family far away would like to see the photos but there are a lot of them and as her child was flower girl, she is in everyone. And then blur a few generic and put those on Facebook.
I agree that she does seem a bit over zealous in the no photos whatsoever remark, which will be interesting when her daughter hits high school and maybe makes the cheer leading squad (you cold also use that argument!) but as sneezing says, she can report every single picture and get them all removed. Take them down and then ask. She muse indertsand that recieivng the ohotos were v exciting and you put them up wi a honeymoon head on.
If she's any sort of friend, she'll realise that it's a honest, excitement in the moment mistake.