You can level the rep with the factions doing PVE only, and then you get a crucible commendation in the package. I believe either they just wanted to force everybody to play PVP, or it just didn't occur to them what they were doing. Just opening the factions to both marks, or glimmer would be the answer. It does suck discarding hundreds of materials, wish you could trade them in for something. I can't believe anybody would ever need to buy them, they are everywhere.