He would surely do it willingly to protect his "brother." I am still on the fence if John is good or bad. I think it will be revealed that is up to his neck in this. Cutting corners and abusing his badge.
Why wouldn't John simply tell Sonny I have been working on this for the last 2-3 years blah blah blah.
All of the leave the rifle stuff also is perplexing. Who shoots someone and leaves the rifle unless they were trying to set someone up to take the fall.
It's a murky/muddled story for sure. So once the mission was accomplished, John was going to just let Jason go home?