Seems like she stayed clear from raising suspicions (by simply not publishing more and going into administration instead) but now she made herself some serious enemies willing to do the work.
The consequences are a matter of trust: A simple office clerk with no scientific training going through the ranks at Harvard growing into "President of Harvard", on the understanding that they "merely" ensure that the business chugs along (and with a proven track record in doing that) while keeping a large part of such administration work off the backs of the scientists and teachers is a better fit than somebody who's demonstrated disregard for the tenets of scientific work.
It doesn't matter why President Gay's works were scrutinized right now, the loss of trust is still real.