As someone who was completely unaware of the project until after the posting of the order, in the year that has passed, I've actually gotten even more peeved about SE's action in retrospect.
Legally, though, SE is on pretty solid ground. That and as much as I disagree with the decision, I can't go as far as to wish the company to fail or to swear them off forever. As horrible as their decision was, they do have the right to protect their copyrighted material. Besides, boycotts don't work any more for a variety of reasons. For instance, I've boycotted purchasing Viacom-subsidiary owned products because of the YouTube lawsuit, but it's not going to stop, say, Iron Man 2 from making money hand over fist.
I am extremely disappointed, though, at the selectivity of their actions. Admittedly I am not aware of the inner workings of SE's legal department, but I refuse to believe that CE got the legal treatment just because it was reported to them -- trust me as I'm sure their legal department gets inquiries and messages every day and there are far more public and well-known fan works SE could have gone after but let slide in willful blindness. I guess the pink elephant in the corner can just get fatter while the Chrono fans get screwed.
I just wish SE were smart enough to tap into this user-created-content model and actually let players create games with a Chrono Trigger style engine for a nominal license or something. Come on, throw the fans a bone.