The ideal would be a more complex system capable of making such distinctions in every situation... but like I said I'm not sure what's possible or not technically speaking, so I'm suggestion a more simplistic approach. Maybe this penalty system could be active only during free roaming and inactive during callouts? I don't know.
Anyway, I'm sharing these thoughts 'cause it's weird that the mod offers so much features and immersion when you're "playing correctly", at the point that you need to use the whole keyboard in a certain way to do that... while lacking the same depth when you decide to "go rogue". I mean, you're a cop that follows a lot of procedures to investigate and pursue criminals while at the same time being able to arrest and kill anyone, anywhere without consequences whatsoever?
Feels like half of the whole experience is missing.