Okay. nobody actually TRIED to explain why they did this, so I will. Post-DLC, they updated the gear vendors with new gear. To get the new gear, you need to obtain, not only marks, but also commendations. The only way to get commendations is to level your reputation (in this case, Vanguard and Crucible). If they had not removed it, you could max your marks out, convert them to materials, convert them to rep, get the package for the commendations. Obviously they don't want you to do this straight away, so you gotta grind out your bounties/strikes or PVP and level your rep the old fashioned way.