If there is academic dishonesty, can I temporarily withdraw from a paper until the dishonesty is removed? I am a PhD student collaborating with a professor (not my advisor). I did the work while the professor came up with the idea and funded the project. The research project centered on an experiment.

Initial experimental results were consistent with Theory A, but they could (with some stretch of the imagination) be consistent with Theory B. Theory B, if proven, would result in a much higher scientific impact.

The professor then decided to conduct a followup experiment. His intention was to provide more support for Theory B. The professor was very excited about the followup experiment, but all the results of the followup turned out to be inconsistent with Theory B. When I updated the manuscript with the the new results, the professor's reply was very brief: "I won't be including results from the followup experiment because I don't have time to look at them". However, he took the time to make further edits to the previous version of the manuscript (with only the original experiment inside) to present the results in a manner such that the original experiment appeared to support Theory B. 

The professor then sent the manuscript to me and asked me if I had any comments before he submitted it to a journal. I protested, but the professor told me that he is the owner of the project as he came up with the idea and funded the experiment. I was told that I can either have the name on the paper, or withdraw completely and irrevocably. 

I do not think this is fair. Is it reasonable of me to say that I do not want my name on the paper now, but I might want my name on the paper in future if the results are (in my opinion) honestly presented?
It is difficult to play hardball when you are a student. I never recommend playing it against your advisor, but this is a bit different as you say. If the person has no effective control over your future then you might consider it, despite the possible blowback. 

What is being demanded of you is unethical. No one can publish your work without your permission. If they publish it without you it is plagiarism. Even publishing it without you as an author but acknowledging your contribution is unethical if you don't agree to having your name used. You have a lot of power here, actually. 

The actions open to you are an ethics complaint to the department or the university. You can also offer to inform any journal to which they submit it without you that they have plagiarized your work. Hardball indeed. 

But a better way is to ask (actually require) them to split the paper. Write a paper that everyone is happy with and make no contentious claims. Have those that are interested write a second paper in which they try to support further claims. The second paper should cite the first, obviously. This isn't the same as "temporarily withdrawing".

Of course, you can also write another followup paper explaining why the further claims are unsupported by the evidence. 

But before you take irrevocable action, make sure your own advisor is in agreement and will back you up in the likely ensuing shoving (and kicking) match. Don't let it come between you and your degree.