Macchiavelli, there is a minor difference. Most people who believe in the Abrahamic religions would probably not exactly agree with the "deserve to be killed" part, and many presumably believe more that non-worshippers will be tortured, as opposed to deserving to be. Teaching a kid that stuff, regardless of his belief, is morally suspect in my book, but for slightly different reasons.
As for 2 and 3, they are potential results of the beliefs proposed in 1, but not necessary. To be sure, they do exist in many countries, and frequently, they are a component of apartheid, but it is not as clear a continuum as you propose. Religions are technically supposed to be bound by their holy books, but in practice, those are ignored to keep the religion viable. Religion is not fundamentally incompatible with a secular society.
Israel is an apartheid nation, for as long as the Palestinian community is treated as intrinsically less important than the Jewish community. Representation in the Knesset is nice, but if they never find their way to government, it is functionally useless.