The edit doesn't really introduce any "logical inconsistencies", it just acts to "remove" the photographer from the scene (by way of removing his other camera), and yet it was ultimately a fire-able-offense.
The photographer, Narciso Contreras had manipulated a photo of a Syrian rebel by using a common Photoshop technique called 'cloning' in order to remove a fellow reporter's camera out of the picture, before sending it to an AP photo desk.
He removed another photographer's camera, essentially exaggerating his own ability to get pictures that other photographers cannot.
It seems to me that photojournalists in general ought to be disclosing any digital editing (especially if it is near the boundary), and it ought to be an editorial decision on the part of the publication on using the photos. The only thing that ever ought to be a firing offense (in this area!) for a photojournalist is undisclosed edits which interfere with ability to make informed editorial decisions.
On the other hand, while I agree that firing might be an extreme response, the edit in question does seriously effect the implied context of the picture. On the third hand, it does so in a way which photojournalist often seek to do through composition, so as you say, the ethics are a bit blurry -- which gets back to why I think disclosure and editorial decisions on whether and how to use photos is more important than blanket policies on edits (digital or otherwise).
http://www.dailymail.co.uk/news/article-2544662/Pulitzer-Pri...
The edit doesn't really introduce any "logical inconsistencies", it just acts to "remove" the photographer from the scene (by way of removing his other camera), and yet it was ultimately a fire-able-offense.