Interesting, guess I've never really run into that specific of an issue.
I generally stop production of something by denying the resources (set trade depots, ores, mines, etc. so they won't deliver resources locally) or turning off the manufacturing component (edit a factory, click the production component's button to turn it off). You won't be able to stop whatever they're manufacturing at the time, but they won't be able to manufacture any more until you re-enable it.