She will eventually have to face the music. In truth, the investigation will probably help your marriage. There will be a report written up for her file. Every CO or change of duty station will expose it. The only way for her to possibly counter the negative (which is a career killer) is to attend counseling and restore the marriage. To basically be able to say "Yeah we had our problems but we got through it and have a strong marriage now. Otherwise she will be looked at by her CO as someone that cannot be counted on when the chips are down or when things get tough. Her fitness reports will always be looked at with a jaundiced eye.