The only "problem" I have with them removing the gear is that they should have said CMs are seasonal to begin with. (don't know if they did) - just like arena, you know it will be over at some point, and Elite transmog sets, Gladiator mounts are unobtainable.
In any case, the end is making me push my limits, picking up classes (prot paladin, resto druid) that I haven't played alot before, to get the sets in time - if you just want to equip your main, and you have good knowledge of your class, watching guides and finding a group on OpenRaid/Guild/OQ will get you the set in a day.
I do like the fact that they will remain prestigious because of not being available, and the difficulty not changing. Even with my issues finding a group to run them. I think all in all it was a great implementation from blizzard. Would even be great if they added different sets for different challenges.
More/faster WoD content > fixing MoP CMs in WoD. More than likely their reasoning, the amount of people who will really care once WoD launches is too small to worry about and not worth their time to fix. Similar to Wrath pvp weapons, tyrannical armor tomorrow and malevolent pvp weapons. The niche who cares is too small to spend development time on it when adding it back in will be controversial in of itself.
It wouldn't surprise me if they bring it back eventually with a "platinum" rank. Or doing something special in CMs. Like doing all the heroic achievements in a run and still get Silver.