Cock-up generally trumps cover-up, Mr Fox. I would be hugely surprised if there was a conspiracy to 'get them off'. I wouldn't be so surprised if there wasn't a little tacit leaning on the APA earlier in the case to ensure that a high profile scalp was in the dock.
I don't think anyone denies that some soldiers behaved criminally and were complicit in the abuse and death of a civilian. What matters is that the right ones are punished and that we have a dispassionate legal system and not a series of show trials.