Ah... "I'm sorry."
That is so much worse. If it was merely ignorance and disgust it would be easier to draw a line in the sand, but Mika did the worst thing possible... she was trying to "help" Kanoko because she blamed herself for allowing her to "become" this way. Family that wants to "fix" their homosexual children and siblings. To consider it a childish phase, wrong upbringing, bad influences... of course that's what it was. That glimpse of Mika being overprotective, the mentions of her being a constant watchful eye and influence on Kanoko for her entire life, it all culminated in the ultimate betrayal. To hurt your loved ones out of a self-centered desire to "save" them can only lead to the worst outcome. Mika probably never understood how far she pushed Kanoko with those words, didn't even remotely comprehend how she ruined her life for years. Just how she never figured out that Shiori was the same as Kanoko and that she was indeed the one she loved.
I think it was amazingly handled. Shiori did exactly what you should do: cut out those who will hurt you, and tell you they are doing it for your sake, from your life. Mika never had the right to meddle with Kanoko's life, to impose her idea of happiness and adulthood onto her. If she had been supportive, maybe Kanoko could have braced herself for the rejection and ignorance that the rest of the world would throw at her. But bereft of the support that family should provide, she only had Shiori to lean on, someone she felt would be hurt by that world all the more. So she pushed her away.
They spent ten years running in circles. At least 7 of those years they were dating, but only now at the present have their minds fully aligned. Ultimately this really was a story about growing up, but those words mean different things to different people. Shiori grew up to embrace who she was, while Kanoko went astray, never being able to fully grow up... not until she accepted the changes she needed to make herself. As a "child" Shiori learned to accept her love for Kanoko, as an "adult" Kanoko learned to accept her love for Shiori.
Pushing people away to protect them, trying to tie people down to protect them, trying to fix people to protect them... all of these are one-sided desires. They only hurt. What is most important is communication and trying to best understand each other. Kanoko and Shiori learned to say what they should say and to express all of these things together. Mika will most likely never learn this lesson and so she has no point of connection to them.
Children are selfish, adults make compromises. A compromise always benefits both parties. Love in its most base essence... is a compromise of emotions. No two people can be the same, but love ties them together, making them want to fit like slightly jagged puzzle pieces that eventually connect.