As for counsel for witnesses, they are allowed to hire lawyers. The lawyers aren't allowed in the room with them, but they are allowed to wait outside, and the witness is allowed to leave the room to consult with their lawyer, even after every single question. It's kind of silly, and I'm not really sure why that's the case, but it's hardly an absurd miscarriage of justice.
Also, Chelsea Manning would still wind up in jail over this if there weren't grand juries in the US, it would just be at trial instead.
No, she has not been pardoned. She received clemency, which is substantively different than a pardon.