If this chapter gives you confused feelings - then it's okay, this is what this chapter supposed to do. To challenge our mindset, to make us think above archetypes.
Mokuren is a very angelic person, she's forgiving and loving, and she always stays true to her beliefs. So even when she got an unforgivable act done to her, she decided to not waver and holded on to her beliefs and forgave Shion. Which, also caused Shion to quesiton himself even more. He's thinking (But i did THAT to her! How can she forgive me!? I don't understand!!) which will be a food for thought to him to eventually understand his mistakes.
As in, we saw Shion's tragic childgood and his poor life with bad decisions he's made because of him not believing anyone. After he gained our sympathy as "Alas, poor boy", he commits an act that we find unforgivable.
This is supposed to make us understand Shion better as well as also open our minds to understanding other atrocious people, to understand WHAT created them, the society, the poverty, tragic past, and then to understand those people and help them to find the good path BEFORE they commit any unforgivable mistakes, and even when they do, to forgive them and help them to understand what they did wrong.