My understanding is that the judge "tossing out the defense" was him declining to dismiss the case outright and sending it to a jury. The jury will likely side with P/CBS, but it's not the same as the judge finding them guilty or anything. Merely that they'll have to try and prove it.
As neither of us have looked through their books we're not qualified to say whether or not they're acting as a 501c. Lawyers and accountants will sort that out. As for me, I'm not out to be their champion. My issues are two-fold. One, I really want to see their film. It looks to me far better than what others (including Bad Robot) are doing. Two, you dumping the whole "ruined it for everybody" on them, as I don't think that's really fair. Paramount, as I said, has been very generous, but they've also refused to offer up any ground rules whatsoever. Axanar does the same things that others have done but on a larger scale and P/CBS decides enough is enough. Fine. Then it enacts (frankly Draconian) rules going forward and says it's all Axanar's fault. Well, there is some basis in that, as they were the ones to finally find out where the line was, but castigating them as solely responsible for killing the goose isn't fair. P/CBS has a good deal of responsibility for what happened, yes, in large part because of their vague generosity, and I think it's largely because of the quality of product Axanar seems capable of producing. That makes them buttheads in my book.