So the following happened when I was doing a SA run at Sapienza: I had retained my SA status until I used the car near Villa Caruso's main gate to exit the mission. The cutscene started playing, where 47 drove the car and hit a random guy standing in the middle on the road and left. This ruined my SA.
Same thing happend in Santa Fortuna. I did everything else with SA and took Rico's car out. Car hit a guard and left. No SA. I reloaded my save and exited via the same exit, this time skipping the cutscene before it could play out. Got SA.
Is this avoidable on the implementation level? Killing NPCs in cutscenes should not affect the rating.