The PHB makes it clear that radiant damage comes from the Positive Plane and is often associated with the Celestials of the Upper Planes, while necrotic damage comes from the Negative Plane and is often associated with Fiends and the Lower Planes
Damage Types (PHB196)
Necrotic. Necrotic damage, dealt by certain undead and a spell such as chill touch, withers matter and even the soul.
Radiant. Radiant damage, dealt by a cleric’s flame strike spell or an angel’s smiting weapon, sears the flesh like fire and overloads the spirit with power.
Positive and Negative Planes (PHB300)
Like a dome above the other planes, the Positive Plane is the source of radiant energy and the raw life force that suffuses all living beings, from the puny to the sublime. Its dark reflection is the Negative Plane, the source of necrotic energy that destroys the living and animates the undead.
Several cleric spells allow you to choose your damage type between radiant or necrotic, and if spirit guardians is the exemplar, you would make this choice based on alignment.
Spirit Guardians (3rd level conjuration)
You call forth spirits to protect you…If you are good or neutral, their spectral form appears angelic or fey (your choice). If you are evil, they appear fiendish. On a failed save, the creature takes 3d8 radiant damage (if you are good or neutral) or 3d8 necrotic damage (if you are evil).
Destructive Wave (5th level Evocation)
You strike the ground, creating a burst of divine energy that ripples outward from you. Each creature
you choose within 30 feet of you…take[s]…5d6 radiant or necrotic damage (your choice)
Forbiddance (6th level Evocation)
You create a ward against magical travel…the creature takes 5d10 radiant or necrotic damage (your choice when you cast this spell).
Other cleric spells do just one or the other type of damage, but there are enough of these that DMs and players making alignment-based choices can find appropriate damage types at most levels:
1st: Guiding Bolt (radiant), Inflict Wounds (necromancy)
4th: Guardian of Faith (radiant)
5th: Flame Strike (radiant), Holy Weapon (radiant)
6th: Sunbeam (radiant), Harm (Necrotic)
7th: Finger of Death (Necrotic), Symbol (Death) (Necrotic)
8th: Sunburst (radiant)
However, at the time of the printing of the PHB and MM, there were no official cleric cantrips that did necrotic damage. This led to NPC's such as the Acolyte (any alignment), Cult Fanatic (any non-good alignment), and Priest (any alignment) being assigned for their principle offensive cantrip sacred flame, which does radiant damage.
Now that Xanathar's Guide to Everything has made official a cantrip that deals necrotic damage (toll the dead), it is possible to replace sacred flame in the stat blocks of evil NPC's with toll the dead.
Are there any balance or other mechanical issues that arise with such a general change?
Are there specific plot issues that might be affected by the use of such NPC's in published modules?
What would the comparative consequences be for keeping sacred flame, but modifying it so that the caster can choose the damage type, as in spirit guardians et al.?
Related: Are positive and negative energy from their respective planes inherently good and evil?
Best Answer
At lower levels, it might cause balance issues
The Monster Manual, under the general text for the Spellcasting trait (p. 10), says:
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.