Batman defied her orders. There is no excuse for that, especially in a situation like the one he was in. He helps them at their pleasure, not the reverse.
And really, past history isn't supposed to factor in. If you're breaking the law, the cops won't let it slide because of past behavior. And given the shit that went down with War Games, because of Batman, I can't blame them (and they have a grudge to hold against Batman, because even if they didn't know it was his plan, they did follow a later plan of his and it blew up in their faces).