I would kind of agree with the other comments on the pacing, which though not bad was slightly 'off' compared to the even wham-wham-wham staccato of episode 2. But thats more because of them having to start bringing in the more 'serious' parts of the novels which are slower than the comedy parts.
About Mikuru-bullying...
1. Kyon's involvement: Actually I disagree that having Kyon take the pictures makes Haruhi even more to blame. If Kyon does take the pictures (like in the novel) it makes him complicit in whatever Haruhi does, whether or not Haruhi did order him to do it or not. In fact, there are many times I spotted in the novels when Kyon could have said something about Haruhi's forcing Mikuru to cosplay but didn't because to some extent he enjoyed seeing Mikuru cosplaying even though Mikuru obviously did not like it. I don't think Kyon's complicity in whatever Haruhi does, no matter how much he insists 'it has nothing to do with me', can be ignored.
2. Frankly the 'computer blackmail' scene isn't that disturbing in the anime or in the novel for me. I couldn't help but laugh. Though of course they are 'cruel', I found most of the Mikuru-bullying scenes funny in the black humor type way but it's actually another Mikuru-bullying scene in the 2nd novel that left me with a bad taste in my mouth and really soured my enjoyment of Haruhi.
Spoiler for 2nd novel spoilers:
When Haruhi whacks Mikuru on the back of her neck so that her contacts will 'pop out' and Kyon stops her saying, "Mikuru isn't your toy!", Haruhi responds, "I've decided that Mikuru-chan is my toy!!" Kyon grips his fist and was only stopped from punching Haruhi by Itsuki.
I did not expect the her to actually use words like that and I found myself wanting Kyon to punch her.