Both Supernatural and Good Omens have missions so obviously canons which borrow heavily from religion and myths are not off-limits.

However, having an Eve who is nothing like the biblical figure, would only be a charge if religious/mythological characters in DF are generally kept recognisable if and when they appear. (I have only read Storm Front so I don't really know anything about the canon.)

If there have been no instances of religious figures making an appearance in canon, it would be a safer bet to just focus on how the Eve is a typical overpowered Sue with an overblown background and how she is distorting canon rather than on how she doesn't fit the biblical description.

Go for it. I have a feeling that some divine retribution should be involved in the assassination, though. *shrug*