There's really no equivalence between a tiny country banning Israeli passport holders and the longstanding conflict over Jewish people being banned from praying on the holiest site in Judaism. Temple Mount has always been a flashpoint for confrontational behaviour between groups to whom the site is significant. If a synagogue had been built upon the holiest site in Islam and Muslims were banned from worshipping there, I suspect the same issues would arise. It would be challenging for Israel to annex the area as administration, visiting and worship there is under Jordanian control.
There are frequent attempts by small, violent groups not representative of the Palestinian population as a whole to prevent non-Muslim visitors entering the site completely, including stopping Jewish people from praying at the Western Wall, and Jewish people were banned entirely from the Western Wall from 1948-67. Does this restriction of movement, access and worship earn equal condemnation?