Yeah, if you click a house, and go into their needs, if you then click on a good, you can restrict it from them. Alternatively, you can empty the good onto a ship every time you get one, because once it's on the ship, your people can't access it. I don't know about how upset they'll get though. Usually, I always have excess of a good, and since I have all the ship upgrades, storage upgrades, and a historic warehouse, each ship can hold 75 of a good, and I can store 500 on my main island.
Just a tip, pearl necklaces are VERY valuable, and a great source of income. Since reefs don't need to be renewed, and you can place many pearl divers to a single reef, you can just setup a huge pearl necklace line, and get some ships to sell them to NPC's.