I think the quote from General Dunlap in that AF Crimes article has the most bearing on the actions taken by Gen Franklin: "If you come to the conclusion the person is innocent, then it would be unconscionable not to try to restore an innocent man to where he was before the accusation was made." I wish all of our commanders had the courage of their convictions on that.
The adultery issue is a separate thing, and I wasn't going to bring this up until you did, but I read the report of the 12 AF/CC-directed investigation of the "love child" that has now been posted to the AF FOIA Reading Room site. The report makes it clear that at the time of the "affair," the Wilkersons were not living together, were having marital problems, and were "physically" but not "legally" separated. As I understand it, "legally" is what counts as far as the UCMJ—but the report glosses over what exactly was meant by "physically." The statement Wilkerson gave to the investigator is not included, so from what is in the report it is impossible to tell if they were physically separated in anticipation of considering a legal separation in anticipation of a possible divorce, or if Mrs. Wilkerson had just gone to visit her parents for a month. And of course the third essential element of adultery under the UCMJ is whether it was "to the prejudice of good order and discipline in the armed forces or was of a nature to bring discredit upon the armed forces." The author of the report, who is not identified, makes a post facto argument that the negative publicity resulting from the disclosure of the "affair" 8 or 9 years later constituted "discredit upon the armed forces," but ultimately relies on the fact that Wilkerson hooked up with the baby momma during a 4 ship RON to HIll that was scheduled after he met the woman—implying that Wilkerson wrongfully used government resources to advance the "affair," which would be "to the prejudice of good order and discipline." But the report's author never really proves that. IMO from the facts in the report, the author could have very easily found no wrongdoing, but perhaps felt compelled to nail Wilkerson on something due to the media focus.
I'm just speculating, but I would hope Wilkerson told all of that to his lawyer, Frank Spinner, at some point, and had a pretty good idea that he was in the clear on that at least legally—and that formed the basis of what he told General Franklin's people. Which was really all he could do if he wanted to get his security clearance back. Anyway, none of that is anything I ever wanted to know about a guy who might have been my commander or IG had I taken some different paths in life... But it is all only tangentially related to the issue of whether Franklin was right to overturn the verdict. And at the end of the day, I still think with 99% certainty that the prosecution failed to meet their burden of proof, and with about 90% certainty that Wilkerson was truly innocent of the charge. Fathering a love child doesn't make you a rapist. If you think it makes it more likely he was simply a cad who was perhaps trying to hook up with the nut job from the Med Group, and got caught, again, it doesn't make him a rapist (and both the prosecution and the defense agreed that the accuser was not so intoxicated as to be incapable of consent). But there are enough problems with the accuser's story that I don't even believe that.
From reading through the documents, I think the only real heroes in this case are Franklin, Breedlove for supporting Franklin, and the Captain ADC who was courageous enough in the appeal documents to call out the O-6 prosecutor for misconduct. Everybody else made fools of themselves, one way or the other (and certain members of Congress and the media are continuing to do so)... But in the American system we aren't supposed to scapegoat people because we're afraid of negative publicity. (See: Duke lacrosse case)