I think I'd take this one to court, too - for all the reasons that Uncle Matt listed. Having been in court a couple of times, I'd be sure to be very polite and respectful, but simply point out the facts. You were trying to be good conservationists by not immediately pushing deer that might escape if you had. You had every intention of tagging your animals as soon as you found them.
You can never know what's going through a CO's mind, so you can't really judge his motives. But sometimes they get confused, and sometimes they are just plain wrong.
Last year a CO walked up on my wife who was sitting in her pop up ground blind and told here that she needed to get some identification on it. I checked the rules and for the Type 1 (Portable Ground Blind) it clearly says, "No identification is required." The only ground blind that requires ID is the Type 3 (Constructed Ground Blinds).
He probably just got mixed up on the different types in that case, but in your situation, it does appear that he was pushing the interpretation of the law to the limits - and beyond. There was nothing in your behavior that indicated anything but what you have said.