For reputation, certain enemies reduce moral immediately by -100 (temporarily) and -10 immediately and fully. Usually non combatants, but the ones that aren't seem to all have certain qualities in common like being affiliated with the Saint.
For example: if you attack enemies during stealth section, its almost always -10 moral per enemy as a punishment for killing unnecessarily. If you kill one enemy its -10, but also an additional -100 temporarily for killing someone in the area since its a crime. If you wait without being scene for long enough, temporary loses go away. So if you start the fight at 0, get -10 and -100 temp, you'll eventually be at just -10.
Edit: this doesn't include the situations where permanent max moral is lowered (too complicated to discuss all at the same time and remain understandable, just understand thats different from this)