remove.cli script does not work. You need to remove items in revers order. You cannot remove driver if some data source is still using it. Please update remove.cli script:

From:
> module remove --name=org.apache.phoenix
> /subsystem=datasources/jdbc-driver=phoenix:remove()
> /subsystem=datasources/data-source=QSPhoenixDS:remove()

To:
> /subsystem=datasources/data-source=QSPhoenixDS:remove()
> /subsystem=datasources/jdbc-driver=phoenix:remove()
> module remove --name=org.apache.phoenix
-------
As far as I know, option 'enabled=true' of 'add' operation for data-source is deprecated in CLI. Moreover, user needs to reload server to be able to use create data source. Please, update the script like follows:

From:
> /subsystem=datasources/data-source=QSPhoenixDS:add(jndi-name="java:/QSPhoenixDS",driver-name=phoenix,connection-url=jdbc:phoenix:127.0.0.1:2181,user-name=sa,password=sa,enabled=true,use-java-context=true)

To:
> /subsystem=datasources/data-source=QSPhoenixDS:add(jndi-name="java:/QSPhoenixDS",driver-name=phoenix,connection-url=jdbc:phoenix:127.0.0.1:2181,user-name=sa,password=sa,use-java-context=true)
> /subsystem=datasources/data-source=QSPhoenixDS:enable
------
Files: hbase-as-a-datasource/README.md, hbase-as-a-datasource/src/scripts/setup.cli
Line: 57 - 3) Setup Phoenix Data Source
1 - --resources=phoenix-4.2.1-client.jar

Please add an instruction to update phoenix version in setup.cli script if user uses different version of phoenix/hbase.