I have no doubt there is more at stake here.
Yes, the CoC can ignore the advice of the JAG office, but in my experience, at least in the Navy, charges are not our first knee-jerk reaction to a problem. Almost every captain I know always asks herself first if there is any other way to deal with a situation, or if there are facts at play that make it absolutely necessary for the good of the service to proceed with a charge.
What I find interesting here is this: It just so happen that the CBC broke the story: How? My guess is she called them in as a strategy to get the charge thrown out, knowing full well all the details she hid from the reporter. Note that this is coming out the week before the court martial, a date she would have known for a much longer period of time, that the starting of Chemo on the same day cannot be a coincidence: She would have known either the date of the CM or the Chemo before the other and could easily have arranged for an absence of coincidence. Finally: looking for sympathy - She already has lost her hair in the news report. I could be wrong but my understanding is that you lose your hair as a result of the chemo - not of the cancer. I know that to avoid the trauma of watching your hair fall, they recommend that you get your head shaved before starting chemo, but she waited after this happened to call the journalists in.
I certainly wish her well in her fight against cancer, but there is just too much missed by CBC here to get my sympathy vote.
The way I see it, Public Relations should make sure that all local journalist are fully invited to witness this Court Martial, so that they have all the facts. That is the only counter to this type of reporting.