I never got the impression that the Rogues of Limsa were being sold to me as Robin Hood types. The guild master is pretty upfront that they're knives in the dark set to enforce the Pirate's Code. They aren't there to rob pirates to benefit the poor of Limsa, they're there to assassinate fellow pirates for breaking the code. Keeping order through the fear of a knife in your back.

On the other hand, they decided to make the reference to thief upgrading into ninja in the original FF game, so that story progression was probly just fated to seem awkward and detached from actual thievery.