Yeah, you need to separate the piece that needs the alpha channel as another mesh. The apply another material to it and use the following settings in the material:
In the Material Basic Parameters set the first drop down to Mask, the second to Blend, check the checkbox 2-Sided, this will give you a possibility to choose a Alpha Mask, and there you put your alpha layered texture map.
Animation Controllers are great when modeling/animating for UDK or Unity3D, or CGI, but, Blizzard rarely uses animation controllers, I only saw them use it for knee positioning on some of the humanoid models. That said, you could select only the bones, not the animation controllers or helpers, and add a animation key to them on the timeline, so that, even if you remove the controllers, everything should still work just fine.