Yes, the presidents of Harvard and MIT should also resign. Because it really does depend on the context.
Free speech is not the unfettered ability to say anything. Free Speech on campus should be balanced against the needs of the students to attend school without threat or harassment. 
Advocating for Genocide is despicable. Although the University is a free marketplace of ideas, calling out for the extermination of Jews on campus is the furthest from a safe and secure space for Jews as there can be. For those presidents unaware of Jewish history, 6 million Jews were slaughtered during the Holocaust. So, Genocide is an exceptionally loaded concept.
The inability to understand the context of this issue and articulate it during an appearance before Congress demonstrates the incompetence of these people to fulfill the role of president at these Universities. If Harvard and MIT are okay with that, that is on them, but they also demonstrate shameful behavior and terrible judgment.