Maybe it's just me, but the way it seems, there is a rise in the amount of essays againt one third of the Trio, and i guess it falls to me to point out a few things. It's weird when people who rush to Dear Percy's defence and blame Arthur for his betrayal and when Hermione shows the same qualities (minus the betrayal, i might add), she is suddenly a vindictive, manipulative witch (pun intended), and the most popular being, a potential murderer. So let's start there.
But really, what choice did Hermione have? Umbridge was about to torture Harry, Hermione didn't have her wand, so it's a given she needed outside assistance to prevent Umbridge from torturing Harry. She couldn't very well take her to Gryffindor Common Room and expect someone to hex her, McGonnagall and Hagrid were not present and Snape had already proved he wasn't interested in saving Harry. So it was either the giant spiders or the centaurs. The fact that Hermione herself didn't know the first thing about centaurs proves that she didn't plan a murder, she just wanted Umbridge out of the way. And they NEEDED Umbridge out of the way, Harry had proof that Sirius was taken hostage. She did what needed to be done, but i doubt murdering Umbridge was on her mind when she led her to the Forrest.
Hermione is manipulative to some extend, but i wouldn't call that a bad thing, since she is rarely manipulative towards Ron and Harry. In PoA, she could have gone behind Harry's back and have his Firebolt confiscated without Harry or Ron knowing it was because of her, but she told them, straight to their faces, that it was her who informed Minerva about the new broomstick. She didn't manipulate Harry into starting DA, she straight out told him without any bullshit, and still didn't give up even after Harry threw one of his fits. Yes, she did manipulate DA members into signing the jinxed parchment, but i'll get to that in the next section.
So she bitch-slapped Malfoy? So what? Ron tries to punch people all the time. So she kept Rita in a jar. Should she rather have shared her bed with her? And she attacked Ron in HBP. It's not that unexpected, she showed every sign that she fancied Ron, and made sure he kept his place in the team, but not only Ron attacked Lavender just to get to her, he (not on purpose, of course) dragged Lavender to the classroom she was sulking in. To Hermione, it must have felt like a slap on the face.
Now, about the jinxed parchment. We should keep in mind that majority of the evidence against Hermione, and Fred and George for that matter, is in OotP and HBP, which are accidentally the books in which Voldemort is back and joined with his Death Eaters. Hermione is a muggle-born, and the best friend of Voldemort's number one enemy. Not only that, but she is also the enemy of Draco, the son of a very important DE at the time. Also, because of her success in her classes, her name is very out there. The way i see it, in a time of war, it is only expected that she would get a bit more violent and seek punishment for traitors, which again, in a time of war, is the worst possible crime. Do I think it's okay to do such a thing? Definitely not. But it is expected, not only from Hermione, but from any person who could be in her position. While many people blame Hermione of being vindictive and cruel, and sometimes going as far as suggesting she could cast a very effective Cruciatus, i might remind you that Harry twice tried that particular spell. She wasn't pretending when she reacted to such a simple spell like levicorpus (HBP, pg: 226), Hermione despises the Dark Arts.
Being raised in a democratic environment, enslavement of any kind would have attracted Hermione's attraction. While i agree that her approach was completelly wrong, what with trying to trick them into freedom, or not giving them the admiration they seek much more than freedom, i refuse to believe she was not genuine in her feelings towards the issue. She was impossibly sympathetic to Kreacher, and she was truly sorry for Winky. It's not the enslavement that's the issue here, but the way some people treat their elves and get away with it. Hermione is right in that regard. I believe, more than anything, Mr. Crouch's treatment of Winky pushed her to take such actions. While it's true that she got a bit carried away with the whole thing, it was not because of a flaw in her character, but because of an honest mistake on her part, which is failing to recognize the real problem.
Is Hermione perfect? Of course not. IMO, her most obvious flaw is accepting what teachers say and books write as absolute truths, and refuse to believe otherwise. She is also at times tactless, and insecure and socially under-developed. And she does make mistakes, one of the most remarkable being not reporting Rita to Dumbledore. But vindictive, cruel, manipulative and ruthless are not her defining features. She is brave, loyal (which Ron failed once in that regard, no matter what his excuses were) and hard-working, and most importantly, she shows the strength to do what needs to be done, whether it be having Harry's broomstick confiscated or getting rid of Umbridge, and what others might think be damned.
PS: Some of my friends in IMDb might ask me, 'Wasn't it you who said you wouldn't want Hermione as a friend or blaming Arthur for the way Percy acted?'. Yes, that's true, and i have given my reasons for both. And i admit i was playing a bit of devil's advocate.