Are you addressing a condition under which Eretz Yisrael is being conquered and is to become Judenrein, and Israelis without dual citizenship would have a problem fleeing?
If there were problem is the diaspora, most Yidden would move to Eretz Yisrael, in which case no passport is needed (the countries expelling Jews wouldn’t require a passport to exit, and the Israelis wouldn’t require them for Jewish refugees to enter).
Neither event is likely. Those Arabs opposed to Israel’s existence are not especially strong militarily and given Israel’s probable nuclear weapon would face mutually assured destruction if they ever attempted to destroy Israel. In the disaspora, while crime is a problem, it isn’t directed against Jews. While the far right favor policies seen as threatening by most Jews, those policies (e.g. support for religious schools, restriction of gay rights, restricting abortion) are seen as favorable by frum Jews. While the far left (“progressives”) favor policies most frum Jews oppose, their policies are against all religions, not just Jews.