Well, if you have a couple of guass cannons and repair stations, you don't have anything to worry actually. Pirates will just suicide against the defenses.
That is an AI problem, not a feature.
The main problem with pirates is that they have no room to make sneak attacks. And they have nowhere to hide. Basically they are unable to act as pirates.
An idea;
So perhaps they should be called mercenaries as you say and just be given a few planets in each game (relative to the galaxy size), making them an always present AI player. They would only go after the bounties and their destruction is not an objective for the final victory.
The one with the biggest bounty on his head would have a large incentive to destroy them, giving him an additional opponent and a "speedbump".
The mercs would also only try to take back the planets they had in the beggining, otherwise they would simply wreak havoc (destroying ships, colonies) to collect the bounty. Otherwise they would act as a normal AI player. What do you guys think?
An additional idea... They could always own a few asteroids that would be placed around the star. This would give the star a strategic importance (resources), the mercs would have a big freedom of operation (stars have many connections) and they would always want to take it back - because of th "rule" they have to always take back their starting places.