It's not like Tuvok told her that she was breaking the Prime Directive in the pilot.
He's been in Starfleet for over 70 years and this is her first week on the job on her first ship and her first mission, so of course she would be so much a grander authority on what is and is not a Prime Directive issue.
But then Kathryn didn't disagree with the Vulcan.
She confirmed his assessment that this was about the Prime Directive, but that she didn't care.
How isn't that criminal?