Correct me if I'm wrong, but wasn't it mentioned somewhere in the novels that Mikoto (like Touma) doesn't prescribe to any religious denomination? Getting her to pray (and with INDEX at that) is kind of unlikely, unless this is set after Volume 22 of the light novels, where Touma goes missing after going after the Power of God, Gabriel.
I think, you can see this picture in context of Vol. 13: Both Index and Misaka try to cure Last Order from a virus, who forced the Misaka Network to create an Artifical Angel.
