At least in 2 jobs I've worked the lawyers came before a lawsuit and said it reasonable to expect a subpoena in the future so we need to preserve a copy of EVERY email/file/paper/whatever TODAY (the day the the lawyer found out). Once you suspect something could be legal evidence in the future you are knowingly destroying evidence. You may not be thrown in jail, but the other side can tell the jury to assume the worst in what you destroyed - and the court can just say "it's your fault for destroying the things you say prove your innocence. Too bad for you."
Unless she is dumber than than any republican on the planet thinks, she had reason to believe that Congress would want to see the emails (not the courts but still a legal issue where subpoenas, perjury, etc apply). And if she was "too busy" to understand what was happening her lawyers, who were involved in selecting emails to delete, certainly know. And they decided to allow her to destroy evidence rather than risk having the emails exposed.
Even if there was not a single email that implicated her in anything illegal or anything that Congress was even interested in, it was "destroying evidence". They can't be used to show her innocence - some questions cannot be resolved either way because of the choice she (intentionally) made.