I hold no brief for Mr Morgan but the "spin" that the current government utilise on any adverse (from their point of view) story would doubtless have played a part in his decision to publish.
If he had referred the pictures to MOD then Cpl Plod would have carried out an investigation and found the pictures were fake. In the time that such an investigation was being carried out the "newsworthy" aspect of the pictures would have diminished and a rival news organisation may have beaten the ragsheet to the story.
We must never forget that HMG do not have a good track record on this sort of story. In (I think) 1942 the Polish Government in Exile published a detailed report on what was happening in Concentration Camps in Poland and the systematic murder of the Jews. That report was rejected by the UK and US Governments.