buildin sites data is initialized by configuration, you can delete, or disable a site by adding extra configuration (using extension machanism - look at gatein document) for UserPortalConfigService. You can find example here: https://docs.jboss.org/author/display/GTNPORTAL36/Default+Portal+Configuration

<external-component-plugins>

    <target-component>org.exoplatform.container.definition.PortalContainerConfig</target-component>

    <component-plugin>

      <name>Add PortalContainer Definitions</name>

    </component-plugin>

    <component-plugin>

      <name>Disable a PortalContainer</name>

      <set-method>registerDisablePlugin</set-method>

      <type>org.exoplatform.container.definition.PortalContainerDefinitionDisablePlugin</type>

      <init-params>

        <values-param>

          <name>names</name>

          <value>classic</value>

        </values-param>

      </init-params>

    </component-plugin>

  </external-component-plugins>

</configuration>