Being Jewish is an ethnicity with a religious component, not merely a religion. We also marry within the tribe, intermarriage is frowned upon. This kept our culture and ceremonies the same over millenia. Our DNA shows we are more like each other than anyone else and indigenous to Israel having descended frim Canaanites.
The example of Indonesian, Afghans and Moroccans doesn't hold up because all they share is a religion, and anyone can convert to Islam. It takes a lot of time and study to convert to Judaism, and it includes Jewish culture, ceremonies, music, food and Israel as our homeland.
As you might know the 1878 Ottoman census was incomplete and frought with methodological problems. However, it shows Jews as a significant population in the cities. Not quite half, but close. By the time the British census was done in the early 1920s, Jews were the majority in Jerusalem.
Regardless, under 400 years of Ottoman rule the Jews had been driven away. There was periodic peace punctuated by attacks and massacres. There was still the enforcement of the Pact of Umar, that said a non-Muslim's court testimony was not equal to a Muslim, that Jews had to subjugate themselves before Muslims, that a Jew could not ride a horse, lest he be taller in than a Muslim, that he could not own a nicer house or a better weapon than a Muslim. Plus pay the extra tax. That was not a situation anyone wanted to live under, so many Jews were driven out.
The checkpoints are absolutely legal. The UN says Israel is occupying that territory. If so, Israel has the responsibility to keep order. To protect both the civilians and the Jews. The checkpoints didn't exist in Gaza for 20 years, that's why they got away with the tunnels and invasion of Israel. Not to mention the brutal oppression of their citizens.