My gr grandmother was a naughty girl. (Civil War)

It's certainly possible though they could have handled the paperwork separately as part of the court case. I would assume the government would want something in the file to ensure she didn't try again later. The only way to know would be to get the file.

Hopefully there's court transcripts, and I would DEFINITELY get a copy of the pension file, as there's bound to be something in there. I've got my own Civil War bad girl. An ancestor came home on leave from the 23 Arkansas Infantry (CSA) after 2 years in service. His wife introduced him to his 3 month old son. 'Nuff said. Still, he survived the war and raised the baby as his own.

Like Michael said--the pension file should have something, quite possibly depositions from witnesses attesting to her remarriage. With any luck there will be documents from the court case in it as well. I imagine the case would have been tried in Federal court. If so, a court case file  should be available through the National Archives in New York City, but be warned--many criminal case files do not include transcripts.

In NYS the OCA is starting preservation / conservation work on really old court documents. Perhaps contact the office of court administration and see what series they're doing if you believe that NYS would have records of this. P.s. Dont worry-- every family has skeletons in the closets!! LOL