What should one do with his/her manuscript after some sort of academic misconduct
I think that the action was a serious breach of trust, but I think there are better ways for the PI to deal with it. If the student didn’t mean malice but published because of inexperience, there should be a way to correct the action and move on.
Concerning a student, I think the best choice is for the student to contact another member of the faculty committee and obtain guidance in how to deal with the PI. I’m suggesting this because the question, while superficially only addressing a paper, cuts much deeper: If your PI advisor is so angry with you as to not coauthor a paper, the relationship may be fractured to the point that efficient mentor ship and guidance has become impossible and the student might be best advised to consider changing advisors.
The answer to the question about the continued membership in the lab will then determine the best path forward for the manuscript as well.