Nothing a bit of story-development couldn't fix, though! I'm in kind of a "writing mood", so lemme take a stab at it...

After the defeat of Good King Moggle Mog, the Moogles are able to restore him to his true, benevolent self. Now, as Real Good King Moggle Mog, he feels the desire to redeem himself, and his people, for the havoc that they had caused while he was corrupted. As such, he asks for a handful of Moogles to volunteer themselves to redeem the name of Moogle-kind! Essentially, you, the player-controlled Moogle, would be among these volunteers, and as far as actual story goes, there would only be a handful who actually volunteered.

Not necessary a case of "becoming a mercenary", so much as being seeking to help the people of Eorzeo and undoing the damage of "Good" King Moggle Mog. Perhaps have a scene in which the rulers of Ul'dah publicly outlaw the hunting of Moogles, and that anyone who is caught will be thrown into the Colosseum.