Of course. But the principle of self-determination is not invalidated if a national group expresses it in a way which don't approve of.
For example, we would support the establishment of an independent Palestinian state even if that state was governed by Hamas and its constitutional basis was Islamic theocracy. The constitution of a state on that basis would certainly imply, to paraphrase your formulation, "a state where [Muslims] have privileges/rights that non-[Muslims] don't have". Nevertheless, we would still support Palestinian independence. So would you, presumably. We would obviously make it our first business to support the struggles of secularists, feminists, democrats, socialists, etc., within that state to radically transform the basis on which it was constituted, but we wouldn't say "until the Palestinians constitute themselves as a democratic-secular republic, they have no right to self-determination."
Similarly, our support for Israeli-Jewish self-determination, the self-determination of what you might call the "Hebrew nation", is not only "activated" once Israel has become "de-Zionised" (to use your rather ugly term, for which you should certainly find a better alternative). Of course we support the efforts of Israeli socialists, anti-racists, etc., to make Israel a state for all its citizens rather than an ethno-nationalist-romantic "state for all Jews", but to suspend our support for the self-determination of the Hebrew nation until that struggle has been won would be sophistry.