A pardon is not possible because she has not been convicted of any crime. She is being held for contempt of court because she refuses to testify to a secret closed door panel. She says she will testify in public about whatever they wish but not to secret proceedings. She has also previously answered the questions they say they want to ask her in the secret proceeding.
Commonly known as "grand jury" and being the basic unit of US judicial system. You are welcome to rebuild the whole judicial system from scratch, but you'd be very naive expecting existing judicial system to cooperate with you on essentially ignoring the law. Usually people who tell judges they don't recognize the law and thus should be treated differently by the judicial system do not fare well. I personally don't believe a judicial system where everybody is free to ignore it at will can function. And thus any "sovereign citizen" types that decides to just ignore the law when it fits them are in trouble.
> She says she will testify in public about whatever they wish but not to secret proceedings
That's not how grand juries work. And the reason for that is that until there's reasonable assurance the crime has been committed or about to be committed, it is improper to publicize information about somebody being investigated, which may harm that person irreparably. If somebody suspects you in a crime, we'd want to be quite sure you're a criminal before we air your private information to the public and call you a potential criminal publicly. That's the function of the grand jury and that's why it closed.
If Manning has any information that needs to be shared, it can be shared independently, regardless of any grand jury. However, the contents of the grand jury proceedings should stay secret, because doing otherwise may harm innocent lives.
Is that true? Wasn't Nixon pardoned for his crimes without actually being convicted of anything? He didn't even manage to get impeached, since he resigned before that could happen.
1. take the stand, be asked one question 2. refuse to answer question, be detained 3. prepare written answer to said question, publish it. 4. take the stand, read prepared answer to said question, be asked another question 5. repeat
It would be tedious, but likely less tedious than spending 500 days in jail with no forward progress.
(Also, her objection is that it is not an "open court")
The way it usually works is if your testimony is needed, you are granted immunity for whatever new crimes that testimony may reveal and are compelled to testify. Then, you can not use 5th amendment as a reason for refusal.
Although if she were going to testify, it would make sense to insist on further immunity, given this grand jury's tendency to conjure charges out of thin air just as IBM conjures fake patents - "X, but with a computer".
I don't think the problem here is that there's some problems with 5th amendment. I think the problem is Manning just doesn't want to recognize the validity of US legal system in general and grand jury in particular. That can only end in one way, and that's the way it ended in.
So yes, she needs to be pardoned again. Or, better yet, just released immediately.