About the use of the moon in "Mysterious Ways", I think I have some info that makes some sense, well at least on one level. There is a play by Oscar Wilde named Salome. It is shaped around the passage in the Bible that talks about Queen Herodias and her daughter Salome, and how she danced for Herod Antipas and got in return the head of John the Baptist on a silver plate. In the song, Johnny refers to John the Baptist (Iokanaan in the play) and the moon to Salome: (I will quote from the play here)
YOUNG SYRIAN: How beautiful is the Princess Salome tonight!
PAGE OF HERODIAS: Look at the moon. How strange the moon seems! She is like a woman rising from a tomb. She is like a dead woman. One might fancy she was looking for dead things.
And then again about the part of "let her pale light in to fill up your room":
YOUNG SYRIAN: How pale the Princess is! Never have I seen her so pale.
Johnny is indeed living underground, he is in prison! And then Salome herself talks about the moon: SALOME: How good to see the moon! She is like a little piece of money, a little silver flower. She is cold and chaste. I am sure she is a virgin. She has the beauty of a virgin. Yes, she is a virgin. She has never defiled herself. She has never abandoned herself to men, like the other goddesses.
And about "to touch is to heal, to hurt is to steal, if you want to kiss the sky, better learn how to kneel", Salome goes to see John and she says:
SALOME: How wasted he is! He is like a thin ivory statue. He is like an image of silver. I am sure he is chaste, as the moon is. He is like a moonbeam, like a shaft of silver. His flesh must be very cold, cold as ivory... I would look closer at him.
And eventually she wants to kiss him but he wouldn't let her. And at the end of the play when John is death, Salome says: (?.) Ah! ah! wherefore didst thou not look at me? If thou hadst looked at me thou hadst loved me. Well I know that thou wouldst have loved me, and the mystery of Love is greater than the mystery of Death.
And THE VOICE OF SALOME: Ah! I have kissed thy mouth, Iokanaan, I have kissed thy mouth. There was a bitter taste on thy lips. Was it the taste of blood... Nay; but perchance it was the taste of love... They say that love hath a bitter taste... But what matter? what matter? I have kissed thy mouth, lokanaan, I have kissed thy mouth. [A ray of moonlight falls on Salome and illumines her]
HEROD: [Turning round and seeing Salome] Kill that woman! [The soldiers rush forward and crush beneath their shields Salome, daughter of Herodias, Princess of Judaea].
Sorry about the long post, I really didn't want to bore you guys! But I had to, since no one had mentioned the Salome/John the Baptist connection. The play is really short, and in it references to the moon appear line after line, so if you want to read it you will be surprised about how it relates to "Mysterious Ways". Which only makes me think that Bono is a genius in writing, as Achtung Bebe said, songs that have multiple interpretations.