Safely steal from shops while invisible

The penalty for killing it is actually pretty small, only one point. Which is regained easily by killing normal monsters. I would not bother to much thinking about it.

Funny detail, killing a peaceful has a -1 alignment penalty. Killing a hobbit has a +6 alignment bonus. So net you gain points. With a big if. You only get the bonus if the hobbit is hostile. So you first need to make the hobbit hostile and not kill it in one hit.

Murdering peaceful humans does have a large penalty. You lose two points of luck and telepathy. Unless you are chaotic, which has no penalty.

If you are doing it for moral reasons, tricking the game into killing it is still breaking your moral code. Bad hacker! No ascension for you.

If this doesn't bother you, you might try using pets, or Traps. Magic doesn't work (and does not give a warning). Perhaps polymorph system shock might work. But not sure on that.

bones is not an option for vanilla nethack.

It is an option, however, in the nethack.alt.org server, which make their source available via git on this repo, if it bothers you.

An alternative would be to reinstall nethack and/or revert any changes to nhdat made after each session of play, though this will also remove high scores, etc. If you kept a copy of the "default" or "clean" version in your home directory, for example, you could copy this over the updated version (containing bones, scores, all other data used in the game) each time your start the game.

Finally, you may un-define DLB during the compile (which is defaulted to on, IIRC) so that the files in /usr/lib/nethack are not concatenated as nhdat and will instead appear as files starting with bones in that directory and you can then remove them manually before or after each play-through.