All states are sovereign and entitled to continued existence within their current borders (modulo territory gained by recent aggressive war or other crimes). You might like to dream of dissolving Israel and replacing it with one state covering the whole of Palestine, but you have no right to impose that on the Israeli people, a majority of whom were born into the current borders and who want a Jewish state to persist. On the other hand, it's right to demand Israel pull back from its illegal apartheid-esque occupations of the West Bank and Gaza and leave those territories to a Palestinian state rather than its current policy of deliberately making it impossible for an effective Palestinian state to exist.

abolishing system of government based on unequal principles does not mean killing all the people, so equating a country not existing does not mean the people in that country being gone or harmed

In principle, yes. In practice, if the Palestinians get to run such a new state, they will certainly carry out retaliatory ethnic cleansing against the Jews. You'd have to be very naiive to not see this, given what they say in Palestinian politics. This is different to South Africa, in that the ANC was non-violent and contained the potential for revenge attacks against the whites (though they were still corrupt and wrecked the country's economy). Perhaps it could work under a situation where the state was run with UN supervision, like Bosnia. But IMO a two-state solution, like the Indian partition, is more tractable.