They have an explanation as to why inhumans are bad but won't tell him, because it's classified? Even assuming the humans are completely justified in their actions because of the explanation, what could it possibly be that they can't just tell him?
You would think the "being mind controlled by criminals for several years" would be enough to explain the low rank compared to abilities but that doesn't work as a plot hook I guess.
"We can't figure out a motive, and she fervently denied it throughout the entire process, but our single witness (a likely traumatized child who didn't even see it happening) says she did it so lets not bother to investigate further."
Is Japans police force incompetent?