In court trials, there is a part of the trial at the beginning in which the question is asked: if we were to assume everything the prosecution says is actually true, do the accusations rise to the level of an actual crime?
It is against the law to put classified information on any system whose classification system is lower than that of the information itself.
Any document written in the line of duty is property of the government, and it is against the law to not turn them over to the government for proper disposition.
Right or wrong, those are the laws. She is accused of breaking those laws. My own time working for the government taught me that with quite a lot of stress and emphasis on document production and classification.
If everything that she is accused of is accepted, her acts rise to the level of prosecution. Now it is the job to conduct an investigation to see if she actually did what she is accused of.