Obviously any song lyric is open to interpretation, and every listener will have a different interpretation, but for people who think that Bono *doesn't* play around with the kneeling entendre, you're missing the boat and failing to appreciate the duality of those lyrics. This is well-known to any U2 fan who reads all the published reviews and literature on Bono's lyrics (i.e., John Waters' "Race of Angels," Bill Flanagan's "U2 at the End of the World," etc.)
From a broader perspective, throughout his entire career, Bono has toyed with the double meanings that stem from juxtaposing romantic/sexual love with religious/God's love. Bono figured out early on that a love song written to a second person audience-- i.e., to a vague, undefined "you"-- can be interpreted both as a love song to God, and a love song to a lover. That's why "With or Without You" works on two levels, as one obvious example.
Also, you're missing the boat if you think that when Bono says that "OOTS" was written for Edge's daughter, that he actually means that every line in the song is directed to her. That's a ridiculous idea, and leads to a perverse interpretation of the lyrics. He just means that the general idea for the song came from that direction. (Look at "Miracle Drug" -- Bono has said he was inspired by Christopher Nolan, as well as the AIDS crisis, when writing that one. He often has multiple muses.)
I think the Madonna connection is interesting, not from a "who-did-it-first" perspective, but to see how artists borrow ideas from one another. I had always thought that Bono's prayer/oral sex (and again, this is not my own, unique interpretation, for the "squeakies" out there, to use another term of Bono's--this is a popular, widespread interpretation) trick was his own, but I didn't see him use it until '91, and I think Madonna's song was released in the late '80s.