Exactly -- "they are looking for any excuse". And by releasing your paper now, you may well have furnished that "any excuse", indeed the "excuse" that will make it seem that they have the moral high ground. As you say, the charges have been made in the 1990s, and ignored by the university. Now that they want to get him on something altogether unrelated, they will conveniently turn to your authority as the lynch pin! You have chosen to phrase the dispute as an accusation of deliberate fabrication, an intentional act, rather than as an academic dispute over what a cited source says or does not say. That accusation, in the current climate, will be taken as "truth", not itself subject to dispute -- and that accusation may well be the rope with which to hang the man.
I don't think you dispute that what would today be called genocide was conducted on native Americans. So, the dispute comes down to whether one particular instance cited as supporting evidence for that is indeed such. You may well be right, and it isn't. But, as an academic, you will know that if anyone goes over footnotes with real diligence, that person will be able to turn up instances of mistaken attribution, wrong citation, a misreading (possibly cross contamination from other material), etc. and can nail that person. Sometimes, it's a case of a citation being considered right at the time, but subsequently shown to be wrong. For instance, Chomsky has been pilloried in some quarters for the figures cited for the effect of sanctions on Iraqi children -- and those quarters will continue to pillory him, even though the main point, i.e., that sanctions did result in considerably elevated dead children, remains valid. They do so in the hope that that main point will be forgotten. It's the same thing with the big to-do over the corruption in the Oil-for-Food Programme. Contrariwise, a person like Niall Ferguson can write a celebration of empire in the 21st century, and be lauded and feted for it.
kj khoo