If the Behavior of the Confederates was inconsistent with their own Charter of Governance, then they are indeed equally hypocritical. I do not know if this is the case, being unfamiliar with the specifics of their Governing charter. I do not know if it had any safeguards for freedom of speech and such.
I do know that the US Constitution did. The best inference that can be drawn here is that the Confederates were "just as bad", but it still does not justify the Abuses of the Union side.
As an example, I do not point an accusing finger at the confederates regarding treatment of prisoners in POW camps because of the equally wretched performance by the north. I would consider it hypocritical to do so.
I have heard that both sides didn't do due diligence in the treatment of prisoners, but I have always heard that the abuses by the South were far worse. Possibly this was the result of them having fewer resources and more hatred for what they regarded as "invaders."
The whole thing was Ugly, and it is a great tragedy that it ever happened.
(once more, with gusto) The observation was not offered with the intention of "justifying" or excusing anything. I merely pointed it out to illustrate that those who lean so heavily on the criticism while ignoring the same "abuse" by the other side (or should I capitalize abuse? LOL) do so without intellectual honesty.