But, if you are tied up fighting elsewhere, you have to tie up resources building defenses on whatever planet they are going to attack...
I've seen the AI put bounty on my head, and then when the pirates attack me, the AI fleet jumps in and attacks the same planet. So, on the whole, I think building planetary defenses where pirates are known to attack makes perfect sense. It will either handle pirates for you "blindly" or if there is a lot going on, delay the pirate attack long enough for you to move a mobile defense fleet into position. If you play against human players, building planetary defenses where the pirates attack is also a good way to "dissuade" the human player from using pirates as a distraction - if they've scouted your defenses, they'll know that this pirate-distraction tactic won't work with you, and if they didn't scout you, then you'll have a surpise for them..
They'll be thinking you are busy dealing with pirates and boom, all of a sudden, you've got a full sized fleet ready for battle..
If you move your capital to where the pirates are attacking, that means you can't have it in another location where you may want it to be.
Err, but wouldn't you build more than one capital at different times, hence, different levels? So while the higher leveled cap is out doing something, the weak(er) one notches up some exp handling the pirates. I still think this is a better deal (return on investment) than spending money on pirate bounty.. 
I've played a few 1v1s where the pirates did play against me. They would be enough of a distraction to keep me from doing exactly what I wanted to.
If in 1v1 against the AI and the pirates are becoming a bigger distraction than you would like, it probably means that you didn't have enough planetary defenses. Like I said, putting 3-5 repair bays + 3-5 hangers + 2-3 Frigs/LRMs and you can almost completely "ignore" a pirate attack at the planet.
However, I am totally in agreement that the fee on your head should go down when you destroy the pirate ships. Maybe not much, but a little. I think it is kinda ridiculous how it only goes down when they kill you.
This is like the Reward Dead or Alive, in the wild wild west
It stays there until they bring you in - dead or alive 
Give it a try.. Maybe you'll learn to appreciate (if not love) ole Jack Sparrow after a while 