Can I get a court case thrown out if it constitutes reprisal due to arrest.

I am having a hard time making sense of this question. Why would there be a TRO hearing in NJ for offenses from a NY court? But in general, whatever the facts of your case are, if you can prove that whatever accusations against you are either false or do not rise to the level of harassment or assault as defined under NJ's Domestic Violence statute, then the case can be dismissed. But you have to do more than simply say that the case was brought as reprisal for the other person's arrest. I think you need to speak with an attorney who handles these types of cases.