No. You can disable a warehouse, but you cannot remove a warehouse. To disable, you must remove all items that are stored in the warehouse prior to proceeding with removal. To remove items, you must either complete an adjustment or fulfillment.
In order to disable a warehouse, simply go to the "Warehouses" page in CommerceJet and select Disable. There will be a message preventing the ability to disable if any items are currently in located at the warehouse in question.