Barney between the eyes:stone cold killer
The decision to kill Barney was a comic display of judicial ineptitude like no other. Slapstick in its absurdity.
Firstly, they neglected to get to the bottom of why* Barney mentioned wendy's death. That was the only issue. The other pieces of evidence were purely circumstantial - in fact they barely form evidence at all. They blithely ignored this.
Secondly, the democratic decision to conceal tom's guilt was the equivalent of taking a spray can to Barney's tombstone. After murdering him in cold blood because leaving him to fend for himself was too inconvenient a moral sacrifice they then allow his friends to continue to belive in his guilt!
Thirdly, they protect Tom after discovering his guilt because he's "too useful". One can infer that they killed Barney because he was of no use to them.
Only great tv can rub one so vigorously the wrong way. Brilliant suspenseful show this notwithstanding.