I don't know, I just think we're all overthinking things here.
In my experience, in most cases, the writers of these shows don't worry nearly as much about clever plot twists with integrity. They just seem to look for a quick wrap-up, whether it is consistent with what went before or not. As an example, as I recall, in Rubicon, members of the conspiracy who stepped out of line were immediately, summarily dealt with: EXCEPT for Will's boss. "24" was the same way, as was House (legal resolutions that strained credulity).
If WE were tasked with coming up with a "Witness for the Prosecution"-like twist to "Killing" then it would probably be something worthy of an extensive discussion; unfortunately, it's the usual set of writers that have to resolve this in one way or the other and I'm afraid we're going to get something much simpler and trite than is being envisioned here.
I hope I'm wrong, of course.
".....and remember, your mission, as always, is to.........kill Hitler!"