There is no valid reason as to why civil and military atc cannot be combined. There is a lot of fluff and bluster but essentially its the same job. Airservices was, at one stage, going to take over the running of non operational bases. Airservices used to provide atc at Darwin until cyclone Tracey.
So why not now? Firstly Airservices wanted to provide the service their way and commercially (this from the people who cant make a profit from a monopoly). Secondly, RAAF middle ranks had to protect their careers so they blocked the move whilst outwardly supporting the move. Along came JBAC to make them more 'essential' within defence.
The reality is that Darwin and Townsville should be controlled by Airservices as they are not R airspace and defence controllers do not have ICAO licences. It is also a reality that most defence controllers will never leave Australia and a large portion are not capable of being deployed.
Having said all that, I wouldnt trust Airservices to run atc at a base unless I had a contract with a lot of clauses about performance and service levels.
Finally, whilst Im on a rant about the system, why not allow towers and arff to be privately operated?