as a preface, I am not suggesting anything.
that said, I believe that this action by SE legal was probably mostly to kill the hype, the word of mouth, the knowledge of the game to the mass market, and also to discourage game modification to the mass market. They don't want the vast majority of gamers to know about this and they certainly don't want more gamers creating content off of their IPs.
As you can see if a project is fairly low key then it gets no attention but when it is making headlines then it is a problem to them, gamers everywhere know about it and therefore they have to address it.
I would say that (and I'm not SUGGESTING it, just speculating) if this hack, or one much like it, were to come out a year or two from now, with no fanfare or publicity, then it would be completely ignored, if it was released to the fans of chrono compendium and other romhacking sites and spread modestly through word of mouth by those people on message boards, IRC, instant message and talking and phoning among friends then it would be ignored like so many other major rom hacks.
the main problem with this was the mainstream visibility, and I don't think it's that out of the question to say that if the same project was released much later, or another project done, that it would be ignored.
Thoughts?
I'm not trying to suggest any action, nor insult anyone, merely thinking about what made this different, I mean there have been many very in depth long hacks done before such as Metroid Redesign and Zelda Parallel Worlds but they had no C&D, I think it is when something is publicized that it really gets into deep water.