They just have to restrict the class ability from the job. In the current beta build every ability has listed what class and what job can use it. It's how people found out that jobs like BLM and WHM won't be using the same abilities as before (BLM now gets ARC + a mystery class, likely ACN, WHM gets THM + a mystery class, likely ACN).
Well therein lies the exact reason why SMN shouldn't have carbuncle. If you want to solo and farm items, you'll be using Arcanist for access to other class abilities like cure, protect, stoneskin, second wind etc. Carbuncle is really for solo play (it has a "tank mode") and that's what classes are for. You'll want to be on SMN for party play, and then you'll be wanting to do as much damage as possible. You won't be soloing on SMN since almost every job is better at soloing as its base class.