To put some specific numbers to it: as soon as a run goes over time its base point value is immediately dropped by two M+ levels, then from there it degrades at a steady clip as time continues to progress over the dungeon's par time.
Even with these penalties though, you can see that someone like Meowchan, has his highest scoring Court of Stars (as of this writing) as a +26 run that went over by 2 minutes:
https://raider.io/mythic-plus/runs/2...court-of-stars (361.96 points). His next highest CoS score was a +23 completed on time, providing 345.69 points:
https://raider.io/mythic-plus/runs/1...court-of-stars