Could have been executed far better, but overall it was good. As someone else mentioned in the comments, could have been worse.
As for the potential message that may have been presented, my thoughts on the matter is: people should mind their own business. If someone wants to dress a certain way, act a certain way, speak a certain way, then so be it. So long as they aren't doing harm to themselves or others then honestly anything goes. The problem lies with other people who are so entitled(or emotional) that they find the need to go out of their way to criticize someone who is different than the norm, and unfortunately the majority of humanity is like that. I suppose it's in our nature to instinctively judge other people to determine whether or not that person is a threat or a boon to our lives, but that mentality tends to get way out of hand when it involves people who don't know better or people who are unwilling to try to understand.
In regards to Miki, it was simply her jealousy that prompted her to attack Yuuko. Given that she is(or rather was) friends with Makoto while somewhat aware of Makoto's circumstances, and Makoto's circle of friends seem to at least be aware of and accepting of Makoto(to what extent I'm unsure), then that means Miki wasn't all that ignorant or unwilling to try to understand, she simply didn't like Yuuko. She definitely didn't have a complete understanding, but her dislike of Yuuko made it impossible for her to want to understand. Of course, using Yuuko's circumstances against Yuuko was clearly a bad decision as it was clearly hurting Makoto, but Miki either wasn't thinking clearly due to her emotions or was still willing to take the risk in an attempt to break them up through indirect means. She should have seen the potential outcome from a mile away should her actions backfire, so she knew what she was getting herself into. She dug her own grave.
As for the other two, Makoto definitely should have been more firm with their words sooner. I understand that it isn't easy to explain things when it will end up unraveling the status-quo and risk destroying what friendship one has, but Makoto needed to stop being hesitant and stand up for Yuuko while also properly explaining things, or at least try to explain. As for Yuuko, while lashing out at someone for being ignorant is far from good, Yuuko likely had already been dealing with shit and their emotions got the better of them. What they said wasn't wrong, but how they went about saying things could have been better. Miki definitely wasn't making it easy.
Overall, they all had problems and all of them went about doing things poorly, some more so than others.
Edit: Would be nice if some time in the future Miki can reconcile with Makoto and can move on from her jealousy. Even if she is still in love with Makoto at that time, would be a good story where she eventually finds someone else whom she can love just as much while still being friends with Makoto. Even better if it's someone that is similar to either Makoto or Yuuko and Miki can become a better person as a result. That is, if the story is executed well enough.
Edit 2: On another note, the "I have an illness called transgender" part pissed me off. I don't blame the author as I'm sure it was intended to be an infuriating scene, but it seems all too easy to assume something like that actually has happened and probably will happen again to someone in the world. Funny how I was talking about intolerance, yet I want to kick that fucking teacher off a bridge cause I'm intolerant of how much of a bigot he was. I'm intolerant of intolerance...would that be considered an oxymoron?
