You can un-publish products from your Crowdship at any time, and you have a couple options to accomplish that.
The "best" way to do it is setting quantity of the product/variants to 0 -- this leaves the product listing in tact in all stores, but makes the product un-sellable as there is no stock.
If that is not desirable, and you no longer want a listing on Crowdship, you can simply remove it via the Crowdship interface on the Products page.
Find the product, select it, and click "Remove from Crowdship."
This will cause the product to be acted on in the Retailer's shop according to their "Supplier Removal" setting, That Retailer setting has these options:
Set the product to Draft (recommended)
Automatically delete the product from my store
It is recommended to only remove products from Crowdship when necessary, as there is no auto-adding back tot he Retailer's shop, and the only way removed products are added back to Retailer's shops is if they manually, by hand add the removed products back when they're available again.