As another has stated, the ATC/Pilot comms quoted are out of context and not in their entirety, it is difficult to get a handle on the exact sequence of events. The ATC work does appear to be sloppy though and Airservices response is an attempt to pull the wool over your eyes. Class D Towers in Australia are not operated as to how ICAO intended and if they were modelled on the way the US runs them? Well, yet more wool pulling.
Having said that, any attempt at apportioning blame to ATC for this accident is spurious and deflection at its best. It may be how the legal system works in Australia? Or how accident investigation works?
Intentional flight into IMC by an unqualified pilot, blatant and intentional rule breaches by the PIC, the ones that can (and did) kill people. Clearly no understanding of LSALT, the list goes on.