Are you sure that was Nintendo's doing? Just off the top of my head, both Castlevania and Ghosts 'n' Goblins had religious imagery and references to death on the NES.
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As far as I can tell the policy was established in the late 80s and lasted through the first half of 90s. Here's a relevant link.
There’s also a relevant quote from Wikipedia article on Actraiser:
According to Douglas Crockford's Expurgation of Maniac Mansion, Nintendo of America had a strict policy regarding game content in the early 1990s, especially in regards to material that could be deemed offensive, a blanket category that prohibited the inclusion of any overtly religious themes or plotlines in a game.
Nintendo of America may not have been consistent, but they were definitely over-strict for some games.