As written, yes.
entitled to a Reflex saving throw (DC 15) each time he is struck by such a weapon [...] success indicates that the wearer takes only half damage
vs.
If she makes a successful Reflex saving throw against an attack that normally deals half damage on a successful save, she instead takes no damage
You could argue that "normally" is not covered by "wearing a special magical armor", but then again, it is normal to have a Reflex save against those attacks when you wear that armor.
At lower levels, it might cause balance issues
The Monster Manual, under the general text for the Spellcasting trait (p. 10), says:
You can change the spells that a monster knows or has prepared, replacing any spell on its spell list with a spell of the same level and from the same class list. If you do so, you might cause the monster to be a greater or lesser threat than suggested by its challenge rating.
Taking your example of sacred flame vs toll the dead, the former forces a DEX save, and the latter a WIS save. Both are major saving throws, so this shouldn't be a problem.
However, using the latter vs. the former against an injured foe increases the damage output from d8s to d12s, which when used against lower level parties might increase the difficulty of the creature, as suggested in the quote above.
My gut feeling is that against Tier 1 parties, it might be better just to swap the damage type of sacred flame to necrotic for that "villain" feel, but against higher level parties, swapping it out for toll the dead probably won't make much impact.
As for the fact that you're changing the damage type of sacred flame, this won't really make much difference; if anything, it makes the spell weaker, since, as can be seen on the table of damage types from this answer, necrotic is more often resisted than radiant. If you were proposing making toll the dead deal radiant damage, that might be more cause for concern, but necrotic sacred flame should be fine.
Finally, for completeness, although I haven't seen/played through all of the official modules, I can at least say that I can't think of any characters for whom this change would make a significant difference. I think with this one, it's a case of common sense at the time on a per-NPC basis.
Best Answer
The “extra damage” is the same type as the weapon’s original damage. This is the same kind of mechanic as, say, sneak attack, just a bonus to the weapon damage you were already rolling.
Holy also, separately from the extra damage, makes the weapon itself good-aligned. This means that its damage, all of it not just the extra damage, is good-aligned and bypasses DR \$x\$/good, as found, for example, on many fiends.
None of the damage is “divine,” “holy,” or “sacred” damage, nor is any of it untyped. Those damage types are quite rare—as far as I know, the only example in core for them is flamestrike.