Another idea: how about a script function, which prevents/enables resting? This function could be used with checks like: if player is inside a certain room/building, they can rest, if not - they can't. Or, when raiders have been wiped out from a certain area, you can rest - if not, you can't.
I would like to preserve the hardcoded resting system if possible, than to script beds and stuff like that with script-driven healing-while-resting options. It would be a much neater solution, IMHO, especially with other modifications I have in mind.