I think it's a matter of taste, not religion, Annraoi. I'm a lay minister and I work in the church several days a week, and I don't like the "religious" lyrics of "De Colores" - I think they're tacky. And I really hate it when people change the words a bit and sing "Holly Holy" and "Bridge over Troubled Water" in church.
I have been told but I'm not sure I believe that Hoyt Axton himself wrote religions lyrics to his "Joy to the World" (Jeremiah was a prophet, Moses was a prophet too). I can't imagine Axton doing this. When our church choir did the song, I went and sat with the congregation and didn't sing.
I guess I have to say I feel uneasy with the use of Gregorian chant as some sort of New Age "healing music" by people who have no understanding or appreciation of the meaning of the scriptural texts sung in chant. I think the principle of religious tolerance includes an obligation to respect what others consider to be sacred.
I also feel uncomfortable with those who take the Christian "fish" symbol and put feet on it and Darwin's name inside. It's like an all-encompassing statement that all Christians reject the idea of evolution, which isn't true. I believe God created through the wonderful natural process called evolution, and that belief is held by many in the "mainstream" Christian churches.
Still, there's always been crossover between religious to secular music, so why not the other way around? See Gospel Origin - Labor & Civil Rights Songs. It appears that even "We Shall Overcome" is an adaptation of a gospel song.

-Joe Offer, still trying to find the origins of "De Colores"-

If I make a quip about Episcopalians and martinis, do you think that will be enough to get Praise to conk me on the head? I thought for sure we'd hear from her by now...