Yes, this is all upside for the accused. However, there is a down side for society. If a powerful person who is offended by anonymous speech can penetrate the anonymity, then no anonymous speaker is safe from being revealed. Being able to engage in anonymous political speech is an important defense against tyrrany.
The conflict here is between the right of the accused to face his accuser, and the right of an accuser to remain anonymous if he wishes. I come down on the side of the anonymous accuser because I feel that anonymous political speech is important to society.
What you're overlooking is that the unmasking is coming after the court has essentially already declared that the speech in question is defamatory (which isn't a protected class of speech). There have been appeals, the anonymous person has sent lawyers to appeal on multiple occasions (which does make one doubt the "it's some random yahoo" hypothesis - Timmy's parents aren't likely to be footing the bills for lawyers to protect his identity). Reading the ruling, it's pretty clear that Mr. X has effectively *had* his day in court, and the judges are basing this ruling on the fact that they believe the posts in questions to be defamatory.
So the system is working pretty much as intended - "Fuboy" (the alias of the person who posted) has had his identity protected through the entire process, and only after substantial judicial review (which includes the judges deciding if the case has merit and a reasonable chance of success - read: it's actually defamation), has authorized revealing the name. Not to mention that at each step, he's had the ability (and has availed himself) of legal representation to attempt to quash the subpoena.
To your root point, I agree that anonymous speech is valuable. But part of that value is that it can't be used as a shield to hide behind when doing actually illegal things.