Hi Dion,
> We are looking to publish a public site from ArcGIS portal using web appBuilder with secure ArcGIS server services
You can create a public app with Web AppBuilder (from either ArcGIS Online or Portal for ArcGIS) accessing secured web services from an ArcGIS Server site. Note that the web map will need to be shared with "public". Based on the information you've provided, this is not a violation of the software license agreement.
If you have additional details around this deployment scenario, you may want to discuss them with your local Esri account manager or Distributor to clarify.
Hope this helps,