If you disconnect a building from the road network, but make sure a serviced road passes one tile from it, it will lose access to the labour pool, but will continue to have service coverage (engineer, prefect). Effectively it is mothballed, but since it can take quite a while before it loses its workers, it is not a very efficient way. It does serve other purposes, one of which will be visible in the main map ...

As GS said, in CIII you can switch off say all clay pits, but that only applies to industries, and for some (wharves, weapons?) it does not work IIRC. The other option is to set priorities for sections with the labour overseer. In later games, like Emperor, players were given more detailed options, but none of them is as elaborate as CIV.