In the military, charges are preferred by an individual's commander, not by a prosecutor. The results of any investigation would bebrought to the person's commander, and the commander would then decide whether to proceed to court martial, offer non-judicial punishment, or take no action at all. In a similar case that happened in 1993, the general officer that insulted President Clinton was given non-judicial punishment (also known as an Articel 15 or Captain's Mast) and fined $7,000. When I was in the Air Force, a person given non-judicial punishment could receive up to 30 days confinement and the loss of two month's base pay, all without ever seeing a judge (hence non-judicial). The individual had the option of refusing the Article 15 and demanding a court martial proceeding.
I would guess that if anything is done to McChrystal, it will be an Article 15 with some loss of pay and he will retire.