I believe most of this confusion is the result of two different storylines colliding, originally the Tarrafal was a "stealth" base meant to monitor the pirates and, depending on how Freeport 2 was handled by the various factions, react accordingly.
The sudden turn to a strike force is a bit rough for two main reasons; the situation in Bering hasn't improved and the Rogue's destroyer, Drunken Codger, is actively trying to assert control over said pirates and remaining zoners which puts them into direct conflict with the Tarrafal.
A fairly unfavourable position for a lone carrier.
