Seriously, you know better, don't you?
This is such a silly argument, I don't why I'm even engaging in it. But...
She can be accused of anything irrespective of who or who isn't her commander-in-chief. And, her commander-in-chief's legitimacy (or alleged illegitimacy) would have absolutely NO BEARING on the factual question of did she or did she not commit a war crime.
Yep, I know what you're going to say - He's not legitimate, therefore all orders flowing from hear are crimes - or some such nonsense. You need to familiarize with a doctrine in American common law called, "De Facto Officer Doctrine". Very simply put, even if someone is in an office that they possibly or absolutely shouldn't be in (or were eligible for) doesn't negate the legality of the decisions they've made. The principle has been upheld in a number of Supreme Court cases.
Moreover, to be convicted of a "war crime" the defendant must be guilty of - you guessed it - a war crime. Taking orders from someone who perhaps wasn't authorized to give them isn't in and of itself a war crime. What you, as a defendant, actually DO is what's determinative. If you commit a war crime, it makes no difference if the person who ordered you to do it was legally installed in their office. Make sense?