This post Possible to color individual BrepFace? asks the same question, and the answer is that it will be available in Rhino 6. That’s now! 
I’m attempting to do the same thing: assigning and querying the material for individual brep faces, but I haven’t been able to figure it out.
I would imagine a MaterialRef would hold both the material, the guid for the brep and a face index. But I don’t see that being the case here: https://developer.rhino3d.com/api/RhinoCommon/html/T_Rhino_DocObjects_MaterialRef.htm
Additionally I don’t understand how to query the MaterialRefs table. If it is a table at all?
Any advice would be greatly appreciated. Thanks!