I'll play devil's advocate here. Every U.S. military installation has a unit dedicated to controlling wildlife, and said unit takes ultimate direction from the commander. This "poacher" in question IS the commander himself, as in the guy who makes the rules. Seeing as how fed rule on a military installation trumps local & state law, I'm betting this case gets tossed out of court within the first five minutes of the first day of hearing.
I've spent my entire adult life on and/or closely affiliated with military installations, and have at times been given the opportunity to hunt an animal. Local &/or state laws do not apply. The goal is to rid an animal or number of animals for the purpose of wildlife population control. It has to be done as part of facility management. If the base in question had to rid a certain number of deer, it would likely either be contracted out to a local pest control business, or the base would have its own in house unit assigned to the job. Either way, inviting the boss(commander) along for a "hunt" is pretty common kiss assery. It's also common for the commander to award hunts to troops or other personnel who have been performing well. If it's a hunt to control deer population, it doesn't matter if the hunter takes a doe fawn or an 11-point buck. It's a deer and counts toward the tally. If any of you were on one of these "hunts", which deer would you pick to shoot?
Given that it was a crossbow fired from inside a truck, on a munitions storage facility, it sounds a whole lot like one of the hunts I just described and as such is well within the commander's authority. Using a crossbow fired from inside the vehicle is the safest, most secure way of performing the task without risking a munitions accident. The feds not charging him is another strong indication that this guy was not out of bounds. Nobody at the top wants the bad publicity of a rogue commanding officer ruffling local feathers. He'd have been dealt with swiftly if he were wrong, more than likely immediately relieved of duty. The story as written just doesn't make sense to me, so I'll reserve my feelings until I find out the final outcome. There just aren't enough details in the article for me to pre-judge. If the guy is guilty then he's made a disgraceful error and should be held accountable. But if he's acting within the confines of his authority, then TWRA and that local paper owe him an enormous apology.