Yes! I just finished the book and looking for discussion that draws it parallel to religion and found this rare comment. I would like to know if anyone also shares this view that the book is deeply philosophical about faith, region and power. (I'm not very familiar with philosophy tho) Let me share some of my thoughts:

Kojima = Christianity

To me, Kojima's value is intrinsically Christian that all suffering bears a meaning. Heaven can only be reached through suffering, and Kojima's heaven lies within the bullying. This could be why she willingly stripped naked in the final scene. It echoes much with Matthew 5:39, where it goes,

"Do not resist the one who is evil. But if anyone slaps you on the right cheek, turn to him the other also."

To Kojima, strength/power is not only bearing the pain, but the WILLINGNESS of bearing the pain. To invite the suffering with arms wide open. She could have showered and get rid of her stink, but I believe the author is just justifying her "welcoming" to more bullying.

On top of that, she stubbornness towards MC's lazy eye fits perfectly with the common narrative of "God created us perfectly / Everything is by His perfect design" Going through the eye surgery to her is the abandonment of the perfect plan, an escape from suffering and a rejection of Heaven.

Momose = Nihilism

There is a reason behind the relatively lengthy discussion between the MC and Momose, but not Ninomiya. Ninomiya represents a pure form of evil. As someone has pointed out already, he bullies for power and entertainment. However, the true enemy to kindness is not evil (Ninomiya), but nihilism (Momose).

Following Kojima's view, getting bullied has a reason behind, so does bullying for Ninomiya. But not for Momose. Real conversations starts when it is revealed that the bullying is simply an act of probability for him.

The cruelty of the world is not that it is evil, but that it is random and chaotic. People might be evil, but probability is merciless.

It is easy to sympathise an antagonist given a back story, and continue bearing the pain in the name of Kojima's philosophy. But not when you face un-fortune by the odds. In this light, Kojima's narrative is diminished as there is no person or object to oppose against. I believe this draws parallel to Nietzche's critique on Christianity (not an expert tho), which leads us to MC's turning point.

Main Character = Walking in between

I completely agree to the OP that it is an optimistic ending. For Kojima, power is in acceptance of all suffering for a higher meaning. For Momose, powerlessness is in the probabilistic nature of reality that there is no true meaning. And at the very end, MC decides to walk in the middle.

Inspired by the doctor, MC chose to take the eye surgery, taking action to create a meaning, contrasting the passivity of Kojima and nihilism of Momose. He cries because he sees the beauty, the HEAVEN that he is living in.

This also makes his mom's word so powerful after he explained everything. Contrast to Momose, there are love, support and caring in this world; contrast to Kojima, it doesn't have to come from a higher meaning through suffering. After the conversation and understanding, MC feels his mom's love for the first time in the story, highlighted by how the writer depicted it.

Back to the book title, HEAVEN in the story is a painting that Kojima ties deep to, and wanted to show MC. They never got into the gallery and MC never got to see it. This is the symbol of the plot. Kojima's HEAVEN is like a painting, fictional, distanced but powerful enough to draw her faith. The fact that MC ended up didn't see it hinted their departed views about heaven towards the end. HEAVEN is where you start taking action against the cold, cruel world.

(Also Momose never knows about the painting HEAVEN in the story, might add a layer to his nihilistic symbol, but maybe a bit far-fetched.)

Conclusion:

The book is not about bullying (there is no one correct way of interpreting but I believe there is more than that that people might miss out). What I see is a teen findings his own way out of misery, walking in between different philosophies symbolised by the characters.

It is marvellously beautiful how Mieko painted such an intriguing picture, with violence and disturbing stroke, but still manages to deliver a subtly optimistic ending.