Nobody has suggesting that setting up an SMTP server is a crime. Heck, nobody has said she shouldn't be using clintonemail or w/e for her personal communications (inc. Clinton Foundation business).
The issue was and is only with her use of a privately run SMTP server for her government job. There's three key problems, first off it avoids FOIA requests, secondly it can avoid other legal discovery, and lastly information was sent through it of a sensitive nature.
And before someone replies with "nothing was sensitive!" if that were true then why has the government redacted and withheld emails from the public? And retroactive classification is largely a myth, things inherit classifications from their source.
So for example if you attend a classified meeting and you or your staff take notes on that meeting, those notes are classified at the second pen touched paper. It doesn't matter than it lacks a classification marking.