My pet theory is that every display of anger Snape ever makes in MOR is part of his act. In fact, the only two genuine displays of emotions we've seen have been his private smile after chewing out Jaime Astorga and his involuntary smile when Harry accused Dumbledore of being a Nazgul. (Snape is the secret Xanatos behind Self Actualization, which is why both Dumbledore and Quirrel keep acting surprised when people assume they're involved.)
Everything actually went according to his plan, except, possibly, being revealed from his Disillusionment as he shadowed the SPHEW members to the ambush. And he DID crack down on all the bullying, he threatened the Slytherins with horrors in private before he publicly punished Hermione.
This is a masterstroke on his part because it removes all incentive the Slytherins and bullies at large might have to seek vengeance against Hermione; she's already being punished severely. The bullies are shamed and fearful, and the one who shamed them is cowed as well. Equilibrium is restored. Hermione pays the price, but it is a fair price, as far as Snape is concerned.
It was Snape that Harry called a Nazgul.
Update: Discussion has moved on to a new thread.
The hiatus is over with today's publication of chapter 73, and the previous thread is approaching the 500-comment threshold, so let's start a new Harry Potter and the Methods of Rationality discussion thread. This is the place to discuss Eliezer Yudkowsky's Harry Potter fanfic and anything related to it.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six, seven. The fanfiction.net author page is the central location for information about updates and links to HPMOR-related goodies, and AdeleneDawner has kept an archive of Author's Notes.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: