Here are my thoughts:
1. Cora is now in the center of two cheating scandals. He apparently was the "orchestrator" of the Astros one, and obviously was the manager during the 2018 Red Sox one. Both teams won the World Series that year, so the MLB definitely is not going to go lightly on Cora.
2. You need to keep Cora until after the penalties are dished out, you can't fire him beforehand. Otherwise, the only way the MLB can punish you is through draft picks and fines.
3. Based on the precedent just set by Houston, Cora will likely be fired after the penalties are handed down--especially if the suspension is for 2+ years. There's no reason waiting for Cora to come back when you can move along with another guy and hope to see him successful in the role. (Jason Varitek!!?)