You dug your own grave by letting anyone own a warehouse when they should have been for official factions. There's no point in having them for official only now, unless you removed the existing ones. Which is just going to provoke a typical upset response.
I'm all for removing existing ones and just refunding the owners what they paid plus extra for any runs they've done. Else you could just make existing WH take longer to produce, materials cost more and take more to produce. Might annoy a few people but makes them less OP than official faction owned ones.