You can't play a criminals' game when you have the morals of a good guy.

He certainly was an antagonist who set the plot in motion with good intentions. The road to hell is paved with good intentions. He was trying to take the moral high ground, but he certainly wasn't the good guy.
As for your metaphor, when was the last time that the USA has taken the moral high ground in anything that we do? Hummel did all of the wrong things for the right reasons, and we (USA) just tend to do kind of a mix of good and bad things for all sorts of good and bad reasons.
You keep calling me Walter. I don't like you. -Rorschach

Stealing chemical weapons would be wrong. Kidnapping people would be wrong. Whether intended or not, his actions lead to the death of the Navy Seals. They also lead to the deaths of numerous men under his command, including the poor guy who got exposed to VX gas during the seizing of the weapons. His actions put in place two scenarios that if not for Mason and Godspeed's involvement would have been massively catastrophic and resulted in the deaths of even more innocents. The first being the bombing of Alcatrez and death of hostages as a response to Hummel's threat. The other being the use of the chemical weapons on civilians in the mainland by the army rangers who fatally overthrew him. His recruitment of these unstable mercenaries was a wrong move. At best, he's a tragic villain with noble intentions but there's the old saying about the road to hell being paved in good intentions.
https://www.facebook.com/angryworld2014/

He did nothing wrong - except from taking 81 innocent people as hostages, locking them up and making them fear for their lives.
And blackmailing.
And aiming weapons of mass destruction on a city.
These minor points aside, he surely was a good guy.