Yes, there were native jews. From what I’ve read there was never a conflict there. The problem came when foreign jews came to settle explicitly to build a jewish state and supplant the local population. They do want an ethnostate. Look at the words and actions of people like Smotrich, Ben-Gvir or go even further back to Herzl, founder of zionism.

I do agree that it’s impractical and immoral to mass expel jews that have settled in Israel for a few generations now; those that are still settling could return to their countries of origin. I do also agree that the only just way forward has to include jews and Palestinians finding some peace living together. I can’t speak for the OP but when I hear the phrase “Israel doesn’t have a right to exist” this is what I understand. Whether you call it Israel, Palestine or something else it cannot continue to exist as a Jewish state. It should grant equal rights and respect to all its citizens. Getting there from where they are now will not be easy but we could start with addressing the international Israel lobby.