We cant really do much with the system. Regardless of the pro-military and pro-civvy trading barbs to and fro, the end result is that these people end up playing "you scratch my back, Ill scratch yours" when it comes to corrupt practices. We all usually end up knowing or hearing of people within both pillars of state who collude on making millions of a particular project.
India has its CAG, which is the independent body you refer to that could do this. But if you really look at it, NAB was supposed to be the embodiment of such a body and currently is itself considered extremely corrupt.
The biggest issue however is, that with the traditional hold of the military(or rather the Army) in the final Damocles sword of "taking over" as has been seen in history, there have been ample occurrences of politicians being caught and taken to task(if rather in a spurious way) as compared to say the military. Spare a few rare cases of being caught, there is very little that was done in the past to actually look at the military's books in the fear that the "buck stops there". However, IMHO if it was so that a proper cleansing of the military was performed and perpetrators punished very harshly, as an exemplar to the politicians that "now even they have no escape". It would send a certain warning out that may reduce corruption and make a push for transparency even further.