According to Reif himself, he signed a "letter thanking Jeffrey Epstein for a gift to Seth Lloyd ... on August 16, 2012, about six weeks into my presidency."
So it would stand to reason that Reif knew about the relationship with Epstein, dating back to at least 2012.
You're ignoring the part where Epstein was a hyper-wealthy socialite who had already made a six-figure donation before his 2008 conviction. MIT administrators have acknowledged that they knew about his crimes and that conviction. They took money from him anyway.
Epstein brought Bill Gates's money through the door. Don't pretend the administration was unaware of his donation history, or that he was just some everyday small-potatoes donor.
Reif had his eyes open, he said thank you for the money, and now he's throwing others under the bus to preserve his own career.
So it would stand to reason that Reif knew about the relationship with Epstein, dating back to at least 2012.