It's quite interesting how it was definitely bullying from how everyone saw it and how it affected everyone and especially Ruri, but Shizuku genuinely believed all the time she was doing something good, all out of misunderstanding comments made about her and taking pride in what she thought were her positive qualities.
Regardless of what Shizuku thought about it, she did bully Ruri. And it's a shame she ended up running away instead of apologizing and trying to make up for it. Honestly, it's hard to root for her when all she's doing is feeling sorry for herself. That's not very sympathetic.
It would be easier if it was just one incident, but how do you apologize and make up for years of cruelty you had thought of as kindness, especially at that age and with all your classmates united against you? She's not just feeling sorry for herself, she's been utterly broken by guilt, to the extent of shunning almost any human contact whatsoever and, as we found out this time, even to the edge of suicide, and a big part of that is exactly that she never got to apologize, something Kaori is finally helping her do now.