On most, if not all, of those, he believed he was within allowances of the law. For instance, the Russian Mobsters he was ready to take to the Supreme Court before Schiff stopped him (admittedly, yeah, he thought it was a longshot, but he still thought the argument could be made). Charging the innocent I'll agree with you on, that was over the line. And as for his motivation, there was a reason he was called Hang 'Em High McCoy; like I said, god save whoever tries to pull one over on him. That said, when he discovered there an an innocent man in prison, he busted his ass to get him freed, despite it going against the law, since he couldn't prove any mistakes or malfeasance during the trial.
Also, the faked prosecution was wholly in concert with the judge presiding over it, who knew full well what the deal was going into it. And half the time he was in contempt for making a point; that also was largely the McCoy fury rearing its head. In any event, I do wholly agree with you on Neutral over Lawful.
Dang I miss that show.