The Boondock Saints is such a brilliant film because you can either just take it all in stride, or actually think about the questions it raises.
One of my problems is, I think too much. :\ Which is only *really* a problem if you can't come up with an answer to all these questions. :S
(Me, I spent my first time watching it drooling all over the twins and their accents. *cough*)
I was too busy doing the happy fangirl squeal over Willem Dafoe as a gay man to really notice the twins. X3 Just add it to the list of things I should be shot for!
About the end... I think it was more of a belated deliverance of judgement than shooting an unarmed man. It was said by the two spectators that Papa Joe "will walk" - and I have no doubt he would have. Thus, Conner and Murphy did what they had to do to stop him because they knew that Papa had immunity when it came to the legal system.
In the court room Papa Joe was easily accessible, unarmed (I've no doubt that Rocco's death had something to do with their decision), and the Saints could deliver their message to the public. In a sense they have a terrorist-like streak in their MO - they wished to install fear in criminals - but then again, they weren't all talk and no action. They had a purpose aside from provoking fear so they can't be considered as terrorists.
Perhaps you're right. I still can't quite put a finger to why this movie disturbs me so much. :S Ah, well...