Whether Shinji gains his self-respect doesn't change anything.
I don't think the Choker was the only thing Kats and Rits intended to punish with, when he is a war criminal and prisoner now.
Even if Shinji stayed at the Wunder, they would've taken further steps to make him suffer.
Matsushiro and N3I alone are enough reasons for Asuka and Kats to torture him and they don't care how honest his apologies are, because he is the very reminder of them failing at being friends and lovers.
But what Kats should know, the same as she failed at being Asukas and Shinjis guardian and preventing Shinji from starting N3I, the bigger she failed to ensure Shinjis imprisonment to prevent N4I, thanks to her arrogance of being only a commanding leader as worse as Gendo. She just represses her mistakes and shoves them to Shinji, so she doesn't have to admit them and gets away with that.
What Shinji 'll fear more than just his punishment and Kats, is of course Asuka herself, because she would punish Shinji herself. That she would 've died in Operation US if Shinji and Unit 1 wouldn't react on her, she didn't even cared that she was calling for him for being about to die. And she was only starring perplexed, for how the very person responsible for her suffering is saving her just now of all times. That doesn't hinder her to demonstrate him her pent up anger and sorrow as she hitted on bulletproof glass in front of his face, while he didn't thought of failing her back then. I don't think that this was the only thing Asuka wanted to do to punish Shinji.
That she's 28 now and Shinji being stuck in Unit 1 for 14 years, doesn't mean that they can see themselves as such. The Curse of Eva makes them perceive their aging and the passage of time as teens. Asuka gaining 14 years more of life and combat experience and she never stopped thinking about Shinji while he has none of that. They're both only Eva Pilots and Asuka being Shinjis guardian instead of Misato wouldn't fit her, because of herself being ready for combat 24/7. It would be more like she is tasked with being Shinjis prison officer, otherwise she would also be his commanding officer the same as Mari being under Asukas command. Asuka 'll never allow him to call her by her name and only addresses her as a captain at her rank, so she can distance herself from this failure of a relationship they have.
The idea of Asuka helping Shinji is totally unimaginable for the situation they are in. She won't care about his wellbeing, when she demands him to follow her orders.
She won't give him the satisfaction to take the easy way out. Dying is too easy for Shinji to happen, when Asuka intends to make him suffer.
And if Asuka does forgive him or even admit her feelings to him, Shinji would be too conflicted with his self-loathing, that he doesn't forgive himself and sees himself unworthy for being forgiven and loved. Even if he knows that she loves him and him to her, he doesn't feel like he deserves her and he only wants to be hated. The only way Shinji wants Asuka to express her love for him is to want her to torture and inflict pain to him.
Even if Kats forgives him, he wouldn't want her to forgive him too.
No matter what happens in FINAL, it doesn't mean that Shinji won't be hurt or that he hurts himself.
The only thing Shinji can do is to suffer, no matter how he accepts himself and lives on.