"incorruptible". What in the hell are y'all talking about?! I'm not saying that the Jim Gordon we have known from the comics is a BAD guy, or even that he isn't justified in a lot of what he does, BUT, he's the police commissioner, sworn to uphold the law, and he actively cooperates with a man dressed as a bat who breaks and enters, commits assaults and any number of other crimes, while operating illegal military grade equipment inside Gotham.
But he's not spending his entire career covering up his own past MURDERS. Why does nobody understand my point that this is a matter of degree, that there is a line between being a morally compromised good guy and being a straight-up criminal? The Gordon of the first season could be plausibly described as the former, but the Gordon of the second season has crossed the line into the latter category.
Look at it this way -- a lot of drinking water has trace amounts of arsenic in it, but that's considered safe if it's below a certain acceptable amount. It's a little bit impure, but not so much that it isn't still acceptable. But if the people in charge of the quality of the drinking water allow the arsenic to rise beyond a certain level, then it become poisoned and they've failed in their job. The same is true here. In the first season, this was a show about Gordon making slight moral compromises, but the levels of impurity were low enough that he could still be considered acceptably heroic. In the second season, though, the writers have allowed that corruption to escalate to an unacceptably high level that has outright poisoned the character. And that means they've failed in their job. They've lost all sense of proportion and taken things way too far.
Although that's part and parcel of the ludicrously high body count that practically every character on the show contributes to. The Penguin is a casual and frequent killer. The Riddler is a repeat killer, even though he isn't in the comics. Even Selina has committed murder, even though Catwoman is generally no worse than a thief and an antihero. The writers on this show can't seem to think of any way to generate drama or tension other than with killing.