A scuttle timer might be helpful indeed. If the had one nobody could complain about some buffing in other areas (if needed) either.
But pirates should only collect on the pirate base to my knowledge, they go back there after a raid afterall... if you are a TEC rebel you can't be raided so they shouldn't collect on your planets either... I could see your enemys being lucky and investing money into a pirate quets for the same planet at the same time, but let's be serious, how likely is that to happen?
So how the hell did you end up with them "expanding" all over the place like this?
Edit: those massive stats could result from one too many successful raid boosting the pirate research too much, maybe looking into the way they upgrade their ships is neccsary as well?