How to remove a corrupted shard in MongoDB
You can use below commands to remove the shards, though I havn't tried ever but looks straight forward.

use admin
db.runCommand( { removeShard: "mongodb0" } )

--Response
{
    "msg" : "draining started successfully",
    "state" : "started",
    "shard" : "mongodb0",
    "ok" : 1
}


link: http://docs.mongodb.org/manual/tutorial/remove-shards-from-cluster