Unfortunately, you have witnessed, first hand, the problem with NY judges who think that they are above the law. It's likely too late now, but there may be potential appellate remedies available (generally, the judges above the trial court level are more likely to do what the law requires, rather than what they personally feel is "the right thing to do"). I wouldn't blame your general counsel though - it sounds more like just the bad luck of the draw when your judge was assigned.
And another consideration, made stronger by the small size of your co-op, is the "broken window" theory. That is, now that there is one problem tenant who suffered no consequences of his actions, the probability of another tenant seeing that and concluding that they, too, are above the rules, goes up dramatically. This is often why you see extreme cases where a Board seeks to make an example of someone. Future shareholders tend to think twice when they believe the Board will come down on them like a ton of bricks!
All in all, being a Board member is a thankless task. Perhaps if you were able to illustrate the issues (financial and otherwise) that your deadbeat has caused the building to the other shareholders, you could drum up enough support for a shareholder vote (as opposed to Board vote) to get them out. Depending on your particular PL, you'd likely need a 66%-75% majority to do this, but the benefit is that as long as the voting was performed as per the lease's requirements, even a liberal Housing Court judge cannot overturn their decision (well, technically, they "could", but as a blatant abuse of their discretion, it would be a slam dunk appeal).