I kind of like this ending. Rika is starting to recover and seems like the cops aren't going to mess with the doctor, so she at least has one positive, adult male figure in her life left. For his part, the doctor stayed a truly good guy until the end, genuinely feeling elated to see Rika recover and even covering for Big Daddy's absence in his speech to her.
As to why Natsumi and Big Daddy decide to keep living on the run - I think the author was trying to be poetic. They have lost everything and no longer have any real purpose to life, but they do have each other. Both of them are basically going to keep living, most likely destitute and always in fear of the law, as a form of penitence. I've seen this trope several times and I think it's decent enough to close their character arcs.
The very last pages with Atsushi going mad is basically the author's way of saying that the cycle of vengeance never actually stops. Just imagine if the main character was Atsushi and Tetsuo was instead the Jason/Leatherface tier villain.
