OP does have a valid point. You either play good guy or play bad guy. You shouldn't be able to appear as a 'clean good guy' if you are pirating or killing other players. As it stands now, the ability to instantly pay off your bounty leaves no room for professional bounty hunters to operate, as 90% of players don't have the cahoonahs to keep their wanted status and simply pay it off as soon as they can.
Needs looking at imo.
Yes. This is true. I think the most straightforward approach is, as was stated, enforce a time limit in cases where the person has committed a crime against another player (who cares about NPCs).
There are workarounds. Escorts in Wings. Catching pirates in the act (even going so far as to set up traps/bait). But, it's still too cumbersome. An 8 hour in-game time limit on player bounties would be great.