There is currently wild speculation as to why the game was removed, but it seems the most prevailing theory is that Valve are unhappy with EA trying to sell DLC without giving them a percentage of the profits. Many think this because of Valve's new Free-to-play friendly policy on steam, in which steam hosts all files but takes a chunk from DLC sales.
There is a problem with that theory though. There are many other games, not owned by EA, that have DLC that isn't available on steam such as Section 8: Prejudice and Dirt 3, both use Games for Windows Live for their DLC, compleatly disproving that theory. Not only that, but both were released after or shortly before Crysis 2 was removed from the store.
This is starting to look like we're on a slow road to all EA games being removed from steam. We're not getting a clear picture on why this is all happening with EA being vague and Valve not saying anything at all. It'll be very interesting to see what happens later on, maybe we'll eventually get some answers, or maybe the two companies will settle this dispute and we'll never hear of it again.