Free resting means the resource game of D&D becomes trivial (i.e. the only challenge left is for a single encounter to be so deadly it threatens to kill a player character; which is a spice best used sparingly), so I'd advise against it.
I'd suggest having the Tomb power the undead to be re-raised every night, making it pointless to kill Tomb Guardians or Withers.
If the repair crews are only "a speed bump" that means next time make them stronger. If this makes the players avoid killing them that can only be for the better (since it is considerably more challenging to avoid/defeat an enemy when you can't simply kill it).
The purpose of having "wandering monsters" as it were is to have a measure of uncertainty; to avoid players going "okay, so this trap will shave 40 hp off my Barbarian, no big deal, I'll still have 15 hp left for when we take a long rest."
With even a small risk of having unexpected visitors during the night, the idea of going to sleep with only 15 hp no longer sounds like such a good idea.
This guides the players into playing the game as it was meant: the Tomb is supposed to be scary, and nothing is supposed to be certain.