Fighting against settler colonists who came and established an apartheid regime is not a crime.

But killing and kidnapping hundreds of innocent civilians is. You have to be clear about that, and also take a nuanced look at the whole conflict. There is no single good or bad side.

Apart from innocent Palestinians and Israelis (good) there are the terrorists (a.k.a. Hamas) who killed and kidnapped hundreds of civilians (bad). Then there is are the settlers, occupying land and terrorizing Palestinians (bad) with the help of the IDF. The Israeli government either looks away or even encourages them (bad). The IDF imprisons children, willingly destroys houses and infrastructure in Gaza and the west bank and executes "precision strikes" in areas of high population while also blocking humanitarian aid (bad).

I support chief investigator Khan's arrest warrant for Netanjahu, Galant, Deif and Haniyya. Regarding the riots after trying to arrest nine IDF soldiers for abusing a Palestinian prisoner, it is obvious that Israel won't be interested in a trial or at least not able to arrange one.

[...] an Israel that provided equal rights to all Muslims, Christians, and Jews living in its territory would be less related to the current state of Israel than modern South Africa is to Apartheid South Africa.

That is my dream. Just people living together peacefully, no matter their religion.