Whatever the wrongs of those higher up in the chain of command my take is that the killing of the priest means Hancock had to get the harshest penalty based on how events were portrayed in the film (and assuming the court became aware of all facts). He chose to interpret Morant's comments as endorsing murder, but that wouldn't be enough to convict Morant.

Regardless of whether Morant was correct or mistaken about the priest being a spy, there was no evidence in the film that Morant had firm grounds to suspect that this was the case (unless I missed something) - at best it was an educated hunch and that should be nobodies idea as sufficient grounds for killing someone. There wasn't even evidence that the higher uppers would have approved of the killing of anyone other than the Boer wearing the British soldier's clothing, so this was going rogue.

I think the film was extremely even handed in its portrayal of the main parties and in its dalliance with excusing extra-judicial slayings in this 'new kind of war for a new century'. But ultimately, the facts of the case completely excuse the firing squad from their actions in the final scene.