Was YouTube also named in the suit? The way I see it, Geller doesn't have the technical ability to "block" any video. He just told YouTube that it was his intellectual property, and they did the blocking or removing or whatever.
Surely YouTube has to be educated (by the courts) on the subject of copyright and fair use. My guess is that some clerk or tech somewhere made the decision to go along with Geller's demand, and now YouTube's legal department might do well to offer some training or oversight of these kinds of decisions.
YouTube wasn't named in the EFF's suit, but the EFF has included a cause of action for declaratory relief, asking the court to issue a judgment that the clip does not infringe any copyright of Geller/Explorologist. YouTube would have no reason not to abide by that judgment, since all it cares about is avoiding liability for contributory infringement.