The incident you describe clearly suggests that there should be some sort of graduated approach to crime and punishment. It seems ludicrous that the punishment for dinging someone's shields is identical to taking them within a whisker of the rebuy screen.
In English law you have three degrees of assault. Common assault could be as little as pushing or slapping someone. That's equivalent in game to dinging a ship's shields so 400 cr fine seems about right.
The next level is Actual Bodily Harm, this involves causing some minor injury like a black eye. I would suggest that the in game equivalent would be perhaps reducing someone's hull by 5-10% or causing significant damage to a module. I think a fair fine would be around 5000 cr but of course we would have to significantly increase the fine for murder.
After that we have Grievous Bodily Harm in which a more serious injury has occurred such as broken bones. I would suggest that the equivalent in game might be reducing someone's hull by more than 25% or completely destroying a module. Perhaps a fine of 50000 cr would be the right level. And maybe the fine for murder should be 500000 cr
A healthy dose of realism would be wonderful. Clearly to make a proper crime and punishment system, if you accidentally attack an NPC, rather than a 400 credit bounty, you should be arrested by internal security and have your ship towed to the nearest starport. At this point you will sit in a holding cell until they confirm your identity and then you can be booked and processed. At this point you can hire an attorney, the best charge 500,000 credits, or be given one free of charge, but he's not nearly as good.
You'll be told you are now being charged with attempted murder and will be executed if convicted, but if you plead guilty to simple assault, you only need to pay a 200 credit fine and perform community service for an hour (4 hours if you got the free attorney) by hauling toxic waste from the nearby station into the nearby sun and jettisoning it there for disposal. After your community service you just need to remember to pay another 20,000 credit fee to the towing agency for moving and storing your ship while you were being processed and can then leave without the sting of a bounty on your head. Seriously why can't Frontier get simple things like this right?