It wasn’t standard operating procedure, she rejected all the stuff the it staff wanted to set up for her. If it had been any other employee of the state department at the time it would have been criminal, and it would be illegal for the SoS today. She also obstructed the investigation.
And it cost her, and the country. It’s probably right she didn’t face charges, but it was still a serious and irresponsible fuckup.
There are levels to these things, and the mar-a-lago shit is obviously exponentially worse.