Rather than disabling it, just rename it by putting a letter on the front of the domain (you can disabling after renaming it if you want) and then Virtualmin will not see an conflicts.
VM will not let you create an alias if the domain is already being used somewhere else.
Nice idea, But that does not seem possible. Going to Edit Virtual Server and clicking on the domain name just takes one to the existing website (so not possible to change it. so for example B.one cannot be renamed aB.one (also I don’t want to destroy all the certs, data, users and email that are currently valid for this domain. It would be just the same as deletion and starting over as a new alias.