The ML is going to be one that finishes off MC's brother. Also he ends up r*ping MC. That was awful and unforgivable. His absolutely s*upid thought process throughout most of the story made it really hard to feel bad for him. He's not super bright as he fails to consider the huge variety of ways he could've ensured all of their safety prior to the rebellion or how to protect ES and EL's wife after. He is a twisted person but you can't say he's evil. I don't hate him entirely but I don't like him at all.

The FL is actually a strong person contrary to what some people think. This is a revenge story and she resolved to survive and kept to her goal. On the other hand beneath her rage she also thought about how her brother wouldn't have wanted her to die hateful and vengeful. But she still feels anger and hate and she still proceeds with her revenge plan. I think her decision to live the way she does at the end of the story came from (a) wanting to live well for her brother who probably didn't actually die hating ML* and (b) knowledge that her brother's death was a conspiracy that would've happened anyways plus acknowledgement ML really didn't want it to happen. (He DID try to stop it when it was happening) Though I can't quite accept how she could love him as much as she once did again.
*ML saved the brothers life before. He was about to be dispatched by highly skilled bandits while unarmed but ML saved him. Before the rebels were going to kill the brother ML urged him to get away. When the rebels began to slow torment him when he refused to abandon post ML ends his suffering. Doesn't absolve ML but it makes him not the worst (?) Starting to think that the suspiciously skilled bandit thing could've been a hint that his death was probably intended by the general to occur during that event.

What I think about the assault depiction

Note. She didn't enjoy what she was going through at all, your body has a physiological response to stimulation and you can't help it. It could've been written in a more horrible way instead of using somewhat "prettier/finessed" vocabulary but I don't think it was meant to glorify the proceedings. Evertime it happened she clearly states that she hates it.

Despite not being able to feel happy for the couple, I can accept what happened. The fact that they end up together doesn't ruin the whole thing for me.

because he wanted at least her body if he couldn‘t have her heart

I also don‘t understand that when he actually didn‘t kill her brother (that‘s how I see it, since her brother couldn‘t possibly have survived that even if he didn‘t give him the last strike), he‘s acting like such a villian and doesn‘t even try to explain. Yes, his reasoning is explained in the story but still it won‘t get into my head why not even try.

I.e. there's not much backstory on the assassination of the previous king which means that I cannot empathise with General Oh and him blaming Eunlib for the death of the former King.

I can see what the writer wanted to accomplish; weaving this common thread of hatred and vengeance through practically every central part of Stigma.

From our MC Eunsoo to even General Oh, (and probably more) their actions were based on vengefulness which lead to even more tragedies that lead to more vindictiveness... (genial!)

If the author had gone through with the FL getting executed after killing General Oh, it would've been much better imo. She would've had her revenge on General Oh by killing him and for ML's revenge, it would be watching her die in front of him without anyway to help her. I don't understand her thought process as to why she forgave him and even still wanted to be happy with him after all the things he put her through physically and emotionally.