Remathilis
Legend
I argue nothing about CR, because CR is irrelevant to the topic at hand. I'm arguing that a given priestess of novice ability can be represented as either a level 1 Cleric, or an acolyte with 2 hit dice. The world still contains the same types of people, whether you use PC rules or NPC rules to represent them.
Given that it's impossible to represent a level 1 Halfling PC with the appropriate Dragonmark, it must also be impossible for that same Halfling to have that Dragonmark if you write it up using NPC rules. Otherwise, it means that NPCs are in-game distinguishable from PCs, with all that entails.
Why doesn't the Acolyte have Channel Divinity? Because he's not a PC. Why does the Gladiator have Brutal as a trait? Because he's not a PC. See how this works?
Your PCs are going to interact with the halfling with a dragonmark two ways: the first is via service ("the halfling uses his mark, you are healed 12 hp") In this scenario, it doesn't matter if the NPC has 1 HD or 100, is CR 0 or 30, or has 1 hit point of 1 million. He's an NPC providing a certain service. Done. The other is if the PCs opt to get into combat with said halfling. At that point, all that matters is that "he's a non-combatant healer, with little more than some knowledge and a magic mark" that the PCs will kill probably in one round. Now, if your PCs comment that "the halfling healer they killed only had 4 hit points and that at minimum, he should have 18 since he should have 4 HD to be equal with a fourth level PC and get a feat", you have a bigger problem than the dragonmark rules.
In essence: any group that can't accept a non-combatant halfling with the mark of healing might be less than equal to a fourth level PC is a group I don't want anything to do with.