Sure, thats exactly what happened, the IT guy screwed up and tried to fix it and accidently deleted something. Because you know, he was an IT guy and I am sure wasn't following the news and had no idea the implication of doing so.
According to Politifacts timeline a subpeona was issued on March 4th. Then, around March 24th they were deleted. So, there may be no evidence that she or her team asked for them to be deleted - but they had 20 days to ask for them all to be retained and to tell him to NOT delete the emails.
At a minimum its grossly incompetent. If a company tried to pull that in a court of law they would be screwed.. 'Oh I am sorry your honor, I forgot to tell IT to not delete all the records you ask for, and so they did it anyway'. Whether she asked or not its an example of a disregard for the law, she obviously made the decision that she would take less political heat deleting them than releasing them, if you think otherwise then you are kidding yourself.