The relevant laws are clear as to what happens. It is the CIO responsible for the individual department who is required to regulate the use of IT resources. It would have been their responsibility to tell Clinton specifically that she wasn't allowed to use the server then cite her if she continued. That didn't happen so she's completely in the clear. The law even allows the CIO leeway to allow things contrary to policy under certain conditions (though I don't think that was done in this case).
The law doesn't provide for felony prosecution for using personal IT resources, no matter how much some people want that to be true for politically convenient reasons. The same people crying about Clinton would reject the charges out of hand if it were their favored political candidate.
In the end she didn't do anything morally wrong which is why this whole email thing has been one big nothing-burger. Everyone has had to fight corporate IT's outdated and stupid policies at one time or another and almost all of us have subverted those policies to get our jobs done.
The only reason we even know about this is because she disclosed it. Colin Powell and Condoleza Rice both used private email servers. So did the entire Bush administration. When confronted with requests for the data they just nuked it from orbit and no one gave a shit. Suddenly it's a huge scandal! The crime of the century!
Trump has violated tax law by using is "charitable" foundation as a piggy bank. I'm not calling for an investigation and prosecution of him because that's banana republic territory.