This saddens me so much that the little girl is being discouraged from doing something so sweet and very innocent at her age.
To tell her to keep her prayers for mommy and daddy just is very, very sad. What she thought was a good thing is being now turned around and in her mind make her think what she did was bad.
I for once would love for someone when they are addessed with an issue like this is to stick up for the one with a belief-prayers, Bible reading, talking about Jesus, etc. Right away it was as if the offended one had all the rights and it better end right there or else. That is just wrong in my opinion.
Also what are you going to do when the parents of the little girl who prayed ask you why she isn't allowed to pray? I know it is very hard to be stuck between the middle but I would have probably told the complaining parent that you don't run a religious childcare but you will have children with it in their life. Then let them know that you are there to provide care for many children and you can't single out one child because of their beliefs.
I had a friend who did run a childcare and had a religious curriculum, prayed, read Bible storie, the whole bit. Everyone in the childcare knew this and then one day a parent decided she didn't want that for her child and would my friend change it. Ah, no I don't think so. The parent finally left seeing she wouldn't win the fight.
So you might be prepared for the parents of the other little girl to have questions for you. You are going to really need to explain it the best you can or you might lose this little girl. You never know how parents may react to something like this or how the little girl may start acting since she may feel like she did something bad.