That implication, although unspoken, is read loud and clear. Kathryn, however, doesn't necessarily agree with it. She appreciates him saying what she cannot bring herself to — that was unbelievably shitty of him (and it was) — but nevertheless rises to Chakotay's defense.

It's impulse at this point, defending her crew. Defending the ex-Maquis. She may or may not have a solid defense already built up to present to Starfleet Intelligence in hopes of preventing them all from being whisked away to a penal colony the moment Voyager crosses Federations borders. (She absolutely does.)

"Perhaps, but he was in command at the time." It's here that she withdraws her hands, laying them on top of one another on the table before her. Shields up, defense mechanisms in place. Closing off as much as she's opening up, always a constant contradiction of herself. "As much as I hate that he disobeyed orders, he had every right to make that decision while I was out of commission."