You come at the question from an excellent perspective. Thank you for the well-thought out reply! It's true that I am not the author. I am the proof reader, and this particular issue was flagged for my review by the first two content editors of the manuscript; both felt that "were" did not sound right to them. But I'm not so interested in what "sounds" right. It's left to me to make the final decision about whether or not it IS right. And to me, that decision hinges on whether or not the construction can truly be considered to be in the subjunctive mood.
To your point, the scene as a whole (versus the single sentence) does add more clarity. This character actually IS certain that his actions are not illegal. There is nothing in the paragraph or scene that would imply he is doubtful of this. He's a police officer and knows the law well. So, in context, when I read the scene I get the idea that he is thinking to himself: "Well, this might be against procedure and might get me in trouble with my department, maybe even fired, but I know they can't actually take legal action against me or arrest me--so screw them. I'm going to do what I think is right."