The author of the article you posted on Plummer, Stephen Manning of the Associated Press,did not write that the chaplain had been vindicated.
But he quotes Plummer's great grand daughter, Olga Plummer Talley, as saying "It seems like its been so many years of our family trying to vindicate him. It finally has happened."

Bottom line: Plummer's record was corrected to reflect an honorable discharge as of late l894. But record of court-martial with sentence and result of dismissal from the army still stands. Further, the Army Board for the Correction of Military Records found no injustice in the trial proceedings and result. The Board, however, approved a posthumous honorable discharge as a matter of "fairness" and "equity"

Strikes me that here a case could be made about the longg after-the-fact application of 2lst Century values to a late l9th Century military trial. Of course, others may take a different view.
But as I noted in my original message--any developments only add to/expands this story. And the story is what history is all about, don't you think?