Have a configurable time interval in which the darkness doesn't hurt the player, handled on a player-to-player basis. Could probably add something in the capability to keep track of this.
Relevant Discord message:
@Shinoow suggestion (if you don't have it already): an initial timer before enabling the mod (per player), so you could make players start taking damage from darkness after 5 days have passed, etc..
For the sake of configurability, have an option to enable/disable this feature.