I'm not an expert on the deployment of Skype for business, but the experience of corporate messenger MyChat can say that this is done in two stages:
1. Import AD users from a domain in the server database. Usually LDAP.
2. Configure transparent authentication of the customer so that Windows users did not enter their usernames and passwords.
If the domain is not used, there is the option of automatic registration at Windows login, but then fail all to quickly deploy the client part using the MSI package, because the GPO is not available without the domain. Will have to come up with something like run the client application from the command line.