From the sound of it, you're playing my Enhanced 4X mod, in which I had to rework both pirates mercenaries and truce amongst rogues. Truce Amongst Rogues does indeed prevent pirates and militia from attacking you in Vanilla Sins, but that caused problems in the mod, so I had to remove it and replace it with allowing you to actually take control of the neutral ships (unmodded they just sit there, you can't control them) and with some bonuses for dealing with the pirates (smaller raids, bounty bonuses), but they'll still attack you. Likewise, outside the mod pirate mercenaries is not free, but is on every culture center, which personally I found worthless since your own ships are better anyways (They were free at one point in the beta though).

Anyways, regardless of if you play a mod or not, Truce Amongst Rogues is their ace card. It provides you either lightning fast colonization or fleet potential, and gives you an advantage you can use to both expand your economy and hinder the enemy's. However, if you're too close to an enemy it might not be possible to use it well, in which case you'll either want to take a balanced approach like the early TEC loyalist or just rush with them (they have bigger bonuses to this in my mod).

The other big advantage they have over the TEC loyalists is the Ragnarov. It's easily better than the Ankylon, with two powerful AoE abilities it can decimate fleets on its own at mid levels and higher, though you'll want plenty of support (repair and command cruisers and a Dunov) and a mop up fleet with it anyways.