You're right, both stories do seem plausible, and we're getting both sides presented through a third party who might or might not have an editorial slant as well. Still, here's the part I noticed more than anything:

"In the fall of 2015, he took a refresher course in the conduct of science, which covered topics such as ethics and misconduct. The course reminded him that, around June 2015, a member of Rubin’s lab had told him about the alleged data fabrication in the Cell Stem Cell paper."

It "reminded him"? As in, someone told him his supervisor was falsifying data, and that didn't warrant even taking notice until something had to jog your memory? While the general circumstances -- student makes false allegations vs supervisor maliciously treats student -- are both plausible, this one line, if accurate in truth and accurately worded, makes me pretty skeptical.