(If I get criticized for this post, it's okay. Like the song says, "everybody must get stoned," which according to Dylan was a reference to the inevitability of being subjected to harsh judgment).
I could believe that. Dylan was always fond of lyrics, titles, and so forth that didn't necessarily mean anything or that were completely arbitrary, but would still be open to interpretation. The title of "Subterranean Homesick Blues" on the same album is one such example; it has no relevance to the song itself.
"Rainy Day Women" is a clear (and I think admitted) reference to Proverbs 27:15, although the numbers 12 and 35 are arbitrary and have long been the subject of speculation. Proverbs is, of course, full of things one might be stoned for doing.
On the one hand, I'm not sure that I really believe Dylan would have just up and written an overt drug song. And apart from that chorus, the rest of the lyrics seem to suggest something else ("They'll stone you when...").
On the other hand, you're right that you can't just adapt the tune, tone and all, for sacred music. There's no way Dylan was unaware of the meaning of "get stoned" in what was then counterculture youth slang. If you hear "Be Still, My Soul," you're not automatically going ot think of Finlandia, which was written as an expression of Finnish nationalism and a protest against Russian imperial censorship. On the other hand, you hear that Dylan tune, and
guaranteed the first thing you think of is "Everybody must get stoned."
The tune was deliberately designed to sound like bad Salvation Army music--in fact Dylan had the musicians play while intoxicated, on purpose. It's made to sound raucous, unpolished, and irreverent by design. It's the antithesis of good church music, which should be reverent, well-ordered, and played with skill.
Of course, I've already asserted that not all musical forms are suited to church music. Everything is not a drop-in replacement for traditional hymnody or the soft pop we associate with contemporary worship music. But there's an assertion in the air that certain chords, instrumental arrangements, etc. carry moral meaning. What I have yet to see is anyone who can interpret that moral meaning. I'm beginning to think it's an empty assertion made to persuade people who don't know music.