Um? The bounty on them is their punishment. It means other players can attack them without themselves getting a bounty on them.
A bounty isn't
punishment for the player. The whole idea, from a gameplay standpoint, of bounties, is to introduce a skill floor for high paying activities like crime. Below that skill floor, taking part in crime isn't worth it as you're going to get caught, but if you are more skilled than that and know getting caught isn't going to happen, then crime can be an option that is more interesting than legal activities.
Now of course, atm the balance between legal and illegal activities is completely out of whack, crime is more risky and requires more skill and effort than legal stuff, and it pays much less, which is a balance failure on FD's part, but they have stated they are working on it.
You don't
punish players for in-game actions apart from the usual insulting/cheating/exploiting. If you have to punish players for somethign they do in game, it means that action should not be possible through the game to begin with. As such issuing bounties on the player isn't the devs making a moral statement about the player, it's a way to make sure only the most skilled/prepared individuals have access to the faster and harder progression paths.
Forcing criminals and only criminals to stay in open until their bounty is gone is however very much making a moral statement about the player. Having criminality be the only path to have structurally differents rules is singling out the players picking that route, very much like FD are singling out the people using cheats by sending them to their own private instances.
A player who gets high bounties has committed crimes. Those bounties are MEANT to be able to be collected by other players. That's their raison d'etre, but in the current system they can be paid off simply, and in 1.3 the player can slip away into a safe group or Solo where other PCs won't attack him for his bounty. If the crimes are committed in Open, or perhaps if they're committed against other CMDRs, then that should imply that the person is open to PvP bounty hunting too to keep the scope of the Open game plausible. Slinking off into Solo until your Bounty expires doesn't really fit that for me.
Pirates feed on traders. These tarders are MEANT to be able to be attacked by pirates to give their juicy loot, it's the raion d'être of piracy. In the current system, they can just ignore pirates completely and run to solo/group where other PCs wont attack them for their cargo. If the trading is done in Open, or perhaps if they affect other CMDRs by chaning faction influence and price in the system, then that should imply that the person is open to PvP pirating to keep the scope of Open game plausible. Slinking off into solo until you feel you no longer need to grind in a helpless T9 and can instead go to solo at the help of a fully kit anaconda doesn't really fit that for me.
Now as you see, I do agree with you in that the whole idea of switching back and forth between solo and open is IMO a terrible thing. Criminals shouldn't be allowed to hide from bounty hunters at will, but neither should traders be allowed to hide from pirates. What I take offense with, is that the system would work differently for one group or the other. Which is why I feel like your character should be locked in one game mode or the other. If you don't want to be bothered by pirates or bounty hunters, fine, pick solo and stick to it. If you want to have a more direct impact on the world around you, pick open and live with the consequences of that choice.