I pose this question, would a holy weapon's enchantment be effective against a good aligned creature who through madness, self perversion or even unknowingly committed evil acts, that in its mind thought were good, or would an unholy weapon be required?
If the alignment has changed to evil, the Holy enhancement would work. If the alignment is still good, the Unholy enhancement would work. If the alignment has changed to neutral, neither will work.
Whether the alignment has changed, and how much, is up to the DM :)
Purely mechanical. If they've got an E in their alignment, holy will affect them.
If the holiness of the sword were obvious, you could wiggle the rules and treat it as illusory damage that will go away, but otherwise, you would require an unholy weapon.