Where's the trouble? Diplomacy. For starters USNA will deny misconduct.

Can deny all they want. There's evidence of it. Japan will change its position. Other countries will follow suit.

Then there's the fact that Japan hid a strategic magician's identity from their ally.

Which wouldn't change the fact that USA has sent operators to allied countries' soil to spy and kill or capture assets.

And if there's anything of an international community, Japan will be outnumbered.

Who says that? There's literally no mention about foreign stances on Japanese-American relationships on the international community.

Makes absolutely no sense to use that as an argument, what if the international community wanted USA out of the map?

Not to mention that killing USNA's strategic magician is the same as tarnishing their reputation and reducing their war potential by taking out their deterrent. In other words, this would be a casus beli to alter the relationship with Japan and seek to eleminate Tatsuya. He wants to protect his sister, not add more enemies that could be after her.

Not correct. There's more than one strategic magician in the USNA, and this strategic magician tried to murder, again, japanese assets.

This is not a casus belli. Killing hostile spies on your soil on defense is not, in the slightlest, close to being casus belli.

Japan needs USNA alliance more than the other way around, because Japan is not on great terms with the Great Asian Alliance and Russia.

That's true, but Japan has the assets to destroy both the GAA and Rusia alone.

As ruthless as Tatsuya is, he's not going to kill without reason. He's not a 90's action movie MC lol.

He literally killed the other soldiers. The only reason he's not killed her is because she's a female character, thus has some plot.