Points For Miki:
Having reread the first volume, Miki's claim actually does have a great deal of credence. She is often seen helping Shoko, informing her on page 80 when the teacher calls on Shoko, and showing her which question the teacher asked on page 69. Bonus points for copying the homework assignment for Naoka when Shoko's questioning caused her to miss what the teacher said (this helps Shoko, albeit indirectly). Additionally Miki does, in fact, tell Shoya to knock it off several times:
Stop goofing off, boys! (Volume 1, page 100, after Shoya dumps a dustpan on Shoko outside)
This happens after Shoya dumps a dustpan on Shoko, who is outside the window.
See? I told you to knock it off! (Volume 1, Page 106)
Miki says this after Shoya injures Shoko by pulling on her hearing aid apparatus. Notably, her alleged first call to "knock it off" is suspiciously missing from the narrative.
Miki also attempts to shield Shoko from harm in several instances. First, when Naoka rudely asks Shoko whether she can speak Japanese, Miki says,
Haha... That's not a nice way to put it. (Volume 1, page 73)
When Shoko asks for clarification for what Naoka said, Miki writes in Shoko's notebook, changing the question to "Do you have a nickname?"
Second, Miki is present when Shoko sees the mean messages written on the chalkboard by Shoya and friends. It's unclear if the message is actually communicated to Shoko since she's deaf, but Miki says,
It's awful, isn't it? I mean, really...(Volume 1, page 97)
In cases where her friends are badmouthing Shoko, it is actually true that Miki does not participate. Rather, she gives diplomatic replies, such as "I know, right?" and "I know what you mean." (Volume 1, pages 105 and 80). She acknowledges her friends' grievances against Shoko, but does not levy any of her own.
Shoya is also shown to be, to a degree, oblivious to the people around him, lending credence to the idea that he might not be the most reliable narrator. When he's doing his daredevil stunts, his two friends show a declining interest in continuing, but Shoya doesn't notice, and it hits him like a brick wall when they outright tell him they don't want to keep jumping off bridges. In high school, he puts mental X's over everyone's faces, further showing that he doesn't pay attention to other people. Since the first volume is almost entirely told from Shoya's perspective, a case might be made that any memories in the narrative he has of Miki being mean to Shoko are fabricated or exaggerated. Thus one wonders whether Shoya's claim on Volume 1, page 124 can be trusted:
And if you count insults, the girls badmouthed her more than anyone! Especially Miki and Naoka!
Naoka, certainly. But Shoya may just be lumping Miki in because she was part of the conversation.
Points Against Miki:
Probably the most damaging point against Miki is her friendship with Naoka, who is definitively known to have bullied Shoko. In spite of this, Miki defends Naoka to the teacher, saying Naoka did more than anyone to keep Shoya in line on page 123. It is possible that Miki just willfully looked the other way when Naoka was bullying Shoko, or, less likely, that she was unaware of the worse offenses Naoka perpetrated. But her strong association with Naoka does lead credence to the idea that she also badmouthed Shoko, even if there is no instance in the manga of this happening.
Secondly, Miki may have been present at the aforementioned blackboard incident when Shoya and friends were writing the messages. On page 95, there is a panel showing the legs of several characters. One pair of socks does resemble Miki's. If so, then this quote would be attributed to her:
When you get in trouble, I had nothing to do with this! (Volume 1, page 95)
She seems to be trying to discourage them, so it's unlikely she took part directly. On the other hand, this means she could have erased the messages before Shoko saw them.
Thirdly, Miki laughed at the Shoya's joke on page 102 about Shoko being deaf because they forgot to write the sutras on her ears. Initially, she does give Shoya a disapproving look, but after the teacher laughs, she laughs too. She even contributes clarification on the joke, saying, "Hoichi the Earless?", and thus giving it her stamp of approval (in her defense, as an honor student, she likely couldn't resist classical/literary allusions).
I suspect that Miki really was doing her best to help Shoko. Her classmates did have legitimate grievances against Shoko, so Miki likely didn't know what to do or who to side with as the class turned increasingly hostile. She didn't stick out her neck for Shoko, so as to keep a target from being put on her, but she did her best to moderate in an impossible situation that could not be handled by children. However, there is a great deal of ambiguity to the character in the story, and I invite everyone to review the character's words and actions and come to their own conclusion.
From an author interview I read in the first volume of the collector's edition (emphasis mine):
Does Kawai take her glasses off [and cry when Shoya accuses her] because she knows she's cute?
Oima: It's a natural gesture. Kawai-san is not that calculating. I'll say this because I want it to be clear: The tears she cries are also 100% pure.
Though it's not canonical to the main story, in the second one-shot, Miki can be seen helping Shoko sing during the choir concert contest. She's holding her hand and giving her some kind of signals. A commentator says:
The girl next to her is showing her which way to adjust her pitch.
Then, when Naoka yells at Shoko and gets a response, and then everyone is badmouthing Shoko by saying she can actually hear, Miki gives a more neutral response:
Well, my mom said she must be wearing a device that lets her hear.
Miki also looks more horrified than anyone when Shoya hits Shoko and causes her to bleed (page 681 in collector's edition, though Miki's drawn kind of strangely). She does wear a smile while the group is leaving Shoya after pushing him in the pond, but this isn't a question about whether Miki bullied Shoya.
The scene where Shoya accuses Miki and Naoka is present in both one-shots as well, with some differences. This indicates Miki was probably always meant to play the role she does in the story. The second one-shot version is essentially the same as in the main story (though lacking Miki's "Why can't we all be friends" line, but in the first one-shot, Shoya only says of Miki,
You were laughing with Ueno, too!
This notably lacks the accusation of Miki badmouthing Shoko. Miki doesn't cry here, but looks extremely nervous about the accusation and says to the teacher,
But sir... I'm the class representative. I would never...
In all three versions, Miki denies any wrongdoing on her part, and none of the versions actually show her doing any badmouthing herself.