Answer
There's no option to disable a command this way, but Workflow Manager's "Clone" feature avoids the problem entirely — clone the currently-deployed workflow version, make your changes in the cloned version, and deploy that new version instead of undeploying/redeploying the original. The command in Page Designer always triggers whichever version of the workflow is currently deployed, so cloning and deploying a new version updates what the existing command runs without ever needing to remove or recreate the Commandgroup item.