Very interesting read so far. I'd just comment before I've digested the whole thing that the study of history and the past in general is rather more reliant upon anecdote and other evidence of lesser quality and quantity than sceptics are typically used to. For that reason it's absolutely packed with mistakes and re-interpretations. It's part of the process.
Even if not stated outright, you should treat
every claim by an historian as just one possible interpretation. With gaps in the evidence of this sort, it becomes a fine line between allowing leeway for interpretation and having rampant speculation of the sort seen in pseudo-history (shameless blog plug
here 
).
ETA - Having read all the way through, the conclusion to draw seems to be that we should exhaust the possibilities with direct reference to the evidence before we start second-guessing motivations and psychology. In this example, historians have offered damning comment without actually applying analysis to the two photographs or the context given by the letters to Fenton's family. The latter suggests that if he
did re-arrange the shot, he made no effort to hide the fact. Looking at the photos, the gif comparison between the two photos
here is very interesting, and the lighting seems to suggest that the photo with the balls on the road was taken before the one without.
My gut reaction to the photo is that the balls on the road
look placed, as they did to Sontag. But I can't quantify that feeling. Objectively, I think they were probably there before the photos were taken. I suspect that we're looking at the same misleading bias-ridden casual attempts at photo-analysis that feed conspiracy theories. The fact that there are two photos is not evidence of deception, and the fact that the balls on the road
look out of place, doesn't mean that they were. The suggestion of deception is a fair enough interpretation to throw into the debate as a possibility, but carries no more weight than any other. It can be criticised, and according to the way history should work, it is being.