Question: What is the actual likelihood that a decorated serviceman, with no prior criminal record (we know this because if Poe had any priors he wouldn't have been in the Army) would actually get prison time for killing two men who attacked himself and his girlfriend? Seeing as there were witnesses (said girlfriend and bartender) I find it hard to believe he would have gotten more than an extended period of probation. A prison term, even a year or two, seems severely harsh considering the circumstances.
Question: Why is there a cache of weapons in the belly of the plane? Is there some reason in US Marshall rules?
Answer: If there was ever an emergency landing the weapons would be needed with the prisoners as they most likely will have to exit the plane at some point. There doesn't seem to be any information around that says that every prisoner transport plane would have the same amount of weapons or in the same spot but it seems likely most would have backup weapons for situations like that.
Question: Why did Poe get back onto the plane when it left Carson city? I know he stayed on after the first stop cause Cyrus wouldn't let Baby-o off and Poe needed to get him his insulin shot. But he got his shot in Carson city and Poe had no reason to get back on (seemed even more ludicrous after he tied the plane up.but anyway).
Chosen answer: Poe is an ex-Ranger, and he wants to stop the criminals. Also he wanted to save the cops inside the airplane.
Question: Why does Cyrus not believe Cusack when he tells him that one of the guards faked a heart attack and that's how they were found out?
Chosen answer: Probably because Cusack interrupted Colm Meaney in the first place. Also he probably knew Cusack would lie about whatever excuse he gave.
Chosen answer: Zero. As you said, he was attacked and there are witnesses that he tried to avoid the fight and the killings were in self-defense. It is an extremely weak plot hammer to get Poe onto a plane full of criminals. It's foolish as well. The writers could have had Poe framed for a crime then exonerated and put in the same situation much more believably.
Grumpy Scot
It's in Alabama. People are put in prison here for much less.
First, Poe is a federal prisoner, not subject to State laws or legal procedures. Secondly, he is not in Alabama. During a conversation with Billy Bedlam we hear that he is incarcerated in the "Q" - prison slang for San Quentin in California. It makes you wonder why a Federal prisoner is in a State prison, but that's another type of mistake.
Would it really be considered self-defense, though? After he beat the guys to the ground he could have just stopped and walked away, but he didn't. He kept beating them until they died.
He is defending his wife against two armed assailants, and use of lethal force is allowable. No DA in the United States would even think about pressing charges, knowing full well a grand jury would throw them out in a second.