I must say that I think that the explanations linked here seem more likely than other explanations I’ve heard.
If “Holy Cow” was related to Hinduism, you’d expect it to have entered the language from England, where they had much more contact with India. I’m not sure that many Americans, back when the phrase was coined, knew enough about India to create an expression intentionally to be disrespectful to the Hindu beliefs.
As for “Holy Smoke,” I always assumed it came from Revelation, not papal elections, because again, most American Protestants back when the phrase was coined probably did not have a great deal of knowledge of Catholic practices, and it wasn’t as if the results of the conclave were broadcast on TV (or even radio, I think) back then.
I myself have been known to say “Holy Cats” without intending any disrespect for ancient Egyptians.
I think the important thing in cases like this is to make sure you don’t intend any offense in what you say,** and to make sure you don’t take unintended offense in what other people say.**
–Jen