There is a legal system. Unfortunately, it's sometimes not enough because of corruption.

[Corruption is especially rampant in Gotham]

And what you saw was in the heat of a government-sanctioned raid.

[Nevermind that the memory also showed the Justice League not being bothered by a military leader yelling at them for moving ahead of his soldiers.

Kirk knows that many of his actions as Batman are seriously morally questionable. It's why he still struggles on thinking if he's just someone making the best out of a bad situation or if he's just a monster making excuses]

I know how it looks. I don't enjoy it.