I wasn't suggesting the results of a Columbia study would be intentionally manipulated because the physics department is worried Kraft might put away his checkbook (one would hope not, at least). More about the optics - if the results are anything less than damning for the Patriots, the media and average fan outside of New England will cry whitewash.
One view I hadn't previously considered came from Fred Kirsch (a Kraft employee for ~20 years) on today's Patriots Football Weekly podcast. He interpreted Columbia's potential involvement in the investigation as a clear shot at Robert Kraft, but didn't want to elaborate.
Taking that view a little further, and I'm admittedly stretching it here, a Columbia study could be a double-edged sword. If it happens to prove Belichick's ball prep & game conditions theory is bogus, not only does Kraft look like a fool, he'll be humiliated by his own university, where he remains highly respected for his involvement as an alumni and his generosity as a donor.
On the other hand, if a Columbia study fully exonerates the Patriots, the fans and media will cry foul over the apparent conflict of interest, thereby leaving the "Cheatriots" narrative to live on and the tarnished legacy of Belichick & Brady to remain.