NB: This is getting into marginal territory for
rule 7 (bypassing DLC purchases). My reading is that it's OK for personal use if you own HF, but you probably shouldn't distribute this kind of mod.
I expect that, if you disable HF, then all
HF-exclusive gameplay features which have a check hardcoded into the engine will cease to function. (The game engine won't let you use some features, even if you remove the relevant DLC checks from the scripts.)
Probably broken/disabled: Bloodlines.
50/50: Sainthood, Sway/Antagonise, Hellenism.
Probably still working: Warrior Lodges (if you have MNM), Eldership (if you have TOG), Coronations.
Obviously, testing would be needed.
I don't think there would be any issues other than disabled features. (But I'm only about 80% sure of this.)