Jade Jaguar
Regular
Ok, here's a new thought I had during my shower just now. A variation on JJ's thesis: maybe the astronaut that shot and killed the doctor was River, who did absorb the regeneration energy, but not child astronaut River. We know the suit was a life support unit, maybe adult River got injured in a story we haven't gotten yet, and the Doctor put her in the suit, and then, knowing the date of his death from the file he got from the tesselact ship, he and adult River arrange for her to kill him and take the energy to save her from dying.
Another interesting possibility.
We know River ends up in prison for killing the Doctor, but despite the killing attempt in "Let's Kill Hitler", she's not in prison at the end. That would suggest that she, in her own timeline, hasn't killed him yet. So, it couldn't have been her in her child astronaut form that killed him at the beginning of "The Impossible Astronaut".
While you've made me way less certain that my original conjecture is true, I still think it might be. I still think it is the infant River in the astronaut suit. Remember, I was thinking that what we see as killing the Dr. was really done to save him, so it might not count as killing him, at least to those who know. We're dealing with time travel, so we'll see what happens.