First, the burden of proof is exactly the same in the military courts: that is, the facts must be proved beyond a reasonable doubt. In fact, some studies have shown that there were more convictions, in general, in civilian courts than in courts martial. The difference is not enormous, but that means that if the judge believes the complainant but has a reasonable doubt, they will acquit the accused in any event, whether the prosecution is in a civilian court or a court martial.
However, in the military justice system, criminal sanctions are not the only ones available. The Canadian Armed Forces have disciplinary powers they can exercise for conduct that civilians are not bound by. It is thus very possible, even following an acquittal resulting from reasonable doubt, for example, for the accused to be subject to disciplinary proceedings of some other kind within the armed forces. There are codes of conduct and prohibitions on their members' conduct that do not apply to civilians.
In my opinion, however, when we are talking about crimes, the same standard should apply to everyone.