The burden of proof is not on the defendant to prove he is innocent, but for the prosecutor to prove he is guilty "innocent until proven guilty." The officers did not investigate the shooting call nor why his blood could be on scene. Bench trials are not real trials, in the sense that it's done on the spot with little preparation. Cops should have done their due diligence to prove he was in fact the one who shot the cops before pressing charges. For example if the cops would have questioned him beforehand, raided his properties, subpoenaed phone records, etc. Then they could have probably proven without a doubt it was him. And not only that, but they would have potentially discovered Tony's and Harry's involvement.

In short, lazy police work should not be rewarded. Cops were capable of doing more to prove it was him but chose not to. In my opinion it's because of judges that hand down guilty verdicts even with enough reasonable doubt. It doesn't matter if he's guilty of the crime or not. IRL innocent people are convicted and guilty people are let go daily.

That all being said this is only my opinion and at the end of the day it's rp. If you are that upset by it then it probably means the show is doing it's job by keeping you immersed and entertained. Just let it happen and watch how the characters handle it, it's not you dealing with it ffs.