Would you rather the MC left her with them? Go in and fight them? He'd have gotten killed and Shiori would have ended up in a worse state. Dude bought her freedom and made sure she no longer had an debt. That's the happiest ending possible.
While there are obvious better ways to resolve it, that would be missing the point. The premise is written in the same measure as the resolution. So none of the story elements you are painting as unsurmountable even need to be surmounted. E.g. He wouldn't need to fight if the debt was held by a bank and she was stripping merely to keep a roof over kanta's head.
For a decent character arc, the idea would be to write a conflict where the MC has agency and/or exudes some type of competence. Not write a linear story where the conflict is so daunting that MC has to just surrender and pray. Naively hoping that giving the bully his lunch money will make him stop sexually and physically abusing his woman. That story is not only unsatisfying for the player but actually makes less sense than just Danny'ing him off.
How? Shiori is indepted, her debt is paid despite how absurd it was, so she is free. Now she has a stable job and a loving and well earning new boyfriend.
She's not free because it's clearly extralegal extortion not real debt. From the type of criminals that just beat and attempted to traffic her. Why in the world would they stop now that they know she hooked someone that can produce large sums of money for her on short notice? Worse, after he has even shown himself scared and defenseless in the actual confrontation?
Mind you, they stated to him that they didn't count the money because they can now find his house and take more money from him at any time. Them owning Mike's ass too now is basically an explicit plot point that merely lacks an in game follow-up event.
