Now that he has made a false official statement, lied to investigators, picked up his brass, and gotten some other agents to lie with him, they are all toast. The best they can hope for is no criminal prosecution, but they can't be agents anymore because the record of this incident would be discoverable in any other case they are involved in.
You wrote:
"Person identified at the traffic stop, known to be armed, flees from the stop, crashes at the road block and comes busting out of the truck.
The two shots in question were fired after the truck crashes into the snow bank, but before Levoy Finicum "comes bursting out". One of them can be quite clearly seen on the phone-camera video shot by the female passenger.
Which makes the FBI agent's position a bit more problematical. You evaluated it this way:
I am betting the FBI agent would get away with those two shots.
My take is that be a good bet only if they took the shots after he was out of the vehicle, or if he brandished a weapon while in the vehicle. Lacking either of those facts it's not such a good bet. If concealed snipers were taking pock-shots at a truck some distance away while all the occupants are still in it and no weapons are visible. That's pretty much "attempted assassination".
Of course the vaunted FBI snipers did do just that (summary execution by sniper assassin) in the Vicky Weaver case and got away with it. So, maybe even with the now-revealed and very bad-looking facts your first statement is still true: "If they hadn't lied, there wouldn't be [any charges]"