Obviously, at some stage someone in the chain of command figured out a mistake had been made in handing over prisoners to the Afghans, and obviously they reported it to someone higher up who was eventually told it was not a problem, when it very much was a problem. The question is: Who was the amoral idiot who decided it wasn't a problem to hand prisoners over to be tortured, and how high up in the government ranks are they? Given the steps being taken to squelch this investigation, I think we can assume it was someone fairly senior, possibly Cabinet level.
The government is doing its best to delay things until they can appoint a new commissioner to the Military Police Complaints Tribunal when the current chairman, Peter Tinsley, reaches the end of his term in December. And they will probably manage to succeed and appoint some useful idiot to shut down the inquiry once and for all.
Which will probably lead the whistleblowers to take the case to the public in bigger and better ways. Eventually, even if it has to wait for a change of government, the truth will out, but it isn't going to set anybody free in this case, except in the sense that they will be free from being tied down to a government job anymore.