Is it my imagination or is Braden embellishing a bit? Near as I could tell the Imperial Captain seemed to think the Envoy fired first, Dar'nala didn't say anything to Braden about Baras. Some random NPC Imperial Trooper says to Baras that Angral thinks its Rebels who planted the bomb that took out the Imperial Captain. Odds are that bomb was a little present from Braden to the Wookiee.

Granted, an assassin tried to take out Baras, and Baras thinks it's Angral. Angral gets the bad information, but he doesn't come across like someone who had just had someone out to assassinate Baras.

I can't tell if this is some clever trick of writing or there are some major plot holes in the comic.

If I might be so bold as to make a statement, I think it's the Emperor. If I remember corectly from one of the timeline videos, or maybe something that I read regarding the story, the Emperor (whoever he is) left the Empire in the hands of the Dark Council in order to persue his own secret goals.
The way of the Sith is betrayal, so it wouldn't surprise me if he is using the Dark Lords for some bigger picture, which will be revealed to us a long time from now when we are playing :D. But then again, who knows what other fiendish things lies in store for us from the Bioware writers. They are doing an excelent job keeping interest up nontheless.