Would you say that it is ok in a game to have human characters that the player can kill without any form of penalty?

Yes. I think there should be consequences for it, but not always a penalty. If that's how the player wishes to play the game, they should be allowed to do so. Arbitrary invulnerability for townspeople or non-player characters isn’t something that caters to evil characters.

These types of characters could be placed anywhere, the important thing is that their deaths have consequences that fit the context of their placement (murder in towns should affect reputation, should affect guard presence, and if the player is seen hurting or attacking anyone, then the town should turn against him).

Again, the important thing is that there is some consequence, but such a consequence is not only a penalty.