Read this article in Haaretz. Notably, the title of the article is a bit misleading. The ex-employee in question did not compare the Holocaust and Nakba, he compared the link between Zionist project and the Holocaust on one hand, and the link between Nakba and the Palestinian national project on the other.
An excerpt from Haaretz;
[The fired employee] Shapira said Yad Vashem chooses to examine only some of the events that took place in the War of Indpendence. "It is being hypocritical. I only tried to expose the visitors to the facts, not to political conclusions. If Yad Vashem chooses to ignore the facts, for example the massacre at Dir Yassin, or the Nakba ["The Catastrophe," the Palestinians' term for what happened to them after 1948], it means that it's afraid of something and that its historic approach is flawed," Shapira said.