That the ninja started out as mercenary commoners is extremely likely, but I think disguise was the real reason that they continued to train with weapons like the kama or kunai. For infiltration and assassination they tended to prefer actual weapon weapons, like the katana; highly versatile weapon/tools, like the kusarigama; and easily concealed/transported weapons like shuriken and blowguns. Either way, though, there was plenty of both good and bad to go around in both the nobility and peasantry in feudal Japan. Ninja could easily be the good guys in any given situation, in a Machiavellian sort of way.
Another thing that sets the ninja apart from a more generalized rogue is the degree of formalized training that they went through. Ninja learned codified techniques for stealth, disguise, espionage, assassination, infiltration, and combat, whereas one tends to think of rogues as being self-taught on the street, or at most apprenticed to a master in more organized environments.