Jonathan, not that it matters to your core point, but as you like definitions and accuracy, the statute in question is the Poultry Products Inspection Act, which is enforced by the Department of Agriculture, not the FDA.
I will note, more to the core of your question, that if you do want to get into the court's basis for its ruling, the preemption analysis is laid out on pp. 9-15 of the opinion (in the link in Jeff's original post). It is pretty clearly written in non-technical language. Had CA merely banned the sale in CA of foie gras produced solely in CA, the statute might have survived pre-ememption, but as it was, the CA law clearly imposes a burden on interstate commerce and states cannot regulate in that case if Congress has imposed its own rules.
The court notes that the PPIA does not require that duck or goose liver be produced only by non-force feeding. CA, by allowing non-force fed duck and goose liver to the sold, and by prohibiting the force-fed variety, it leaves open the possibility that producers and sellers who comply with Federal law can nonetheless be in volition of CA law. Preemption does not allow that; hence the court had to strike down the CA law.
It probably doesn't help respond to your sense of what is right and wrong, but i don't see a practical way to put the Constitutional issues aside in this situation.