I don't think it's about 'destroying' countries, but rather, countries that may have flawed principles or injustices correcting these and - for lack of a better term - improving their 'brand image'.
The US did this with slavery. Was the US wiped off the map or 'destroyed'? Well.. a civil war did result, but the point is the country went through a period of reckoning and evolved into a country that finally abolished that practice (obviously the US was essentially still an apartheid state with Jim Crow up until the 1970's as you've pointed out, but that too was eventually done away with). Did the US cease to be the US? No.
Same with apartheid in South Africa. The country of South Africa still exists. The people still exist in that country. It wasn't 'destroyed'. But, it did change itself to get rid of a cancer that was not conducive to civil liberties and freedom.
I don't think Israel needs to be 'destroyed'. But, it too has things it needs to reckon with that might aid in peace and healing, and encourage greater democracy and freedom. The fact that an Arab can't travel freely (or at all) from Gaza to Tel Aviv is not conducive to a truly free society. Neither is its ban on interracial marriage (something the US also banned in many states up until around the 1970s).
Does Israel have a very difficult situation with balancing security with freedom? Absolutely. But... perhaps some of this is due to Israel's insistence on building an identity around 'Jewishness' that alienates those that aren't Jewish, and imposing religious restrictions as law (which is quite incompatible with many Western ideals of freedom).
The fundamental problem of Zionism though - as I've mentioned before - is that it's really boxed itself into a corner, both geographically and ideologically. The reason interracial marriage is banned in Israel - as far as my understanding goes - is that it would threaten the Jewishness or Jewish identity of Israel. Zionism has built its whole identity around being Jewish and Jewish self-determination. Yet, this puts it in direct conflict with many democratic principles. It's trying to be a democratic theocracy and this is proving to be a very difficult thing for it to cling onto without granting freedoms that could potentially conflict with the 'purity' of its Jewish identity.
Another example: Israel wants Jewish self-determination. But, it also allows Arabs to run for seats in the Knesset. This is a conflict and contradiction waiting to happen. How many seats can Arabs hold before a panic over identity sets in and Israelis worry that their Jewish self-determination is being compromised to allow Arabs to sit in the Knesset? Fundamentally, Arabs and non-Jews will always be at a disadvantage in such a system, especially in cases where preferential treatment is given to 'believers' of the 'correct' faith (i.e. hiring practices, housing, etc.).
By the way, Islamic theocracies have the same contradictions and tend to solve them by simply being extremely authoritarian. Israel is resisting this in some ways better than - say - Iran. However, the situation in Gaza and the West Bank show that this deadlock between 2 fiercely tribal and religious groups that are obsessed with preserving their own 'national identity' on the same land with no willingness to cede ground or set aside ambitions of their very own theocracy.. is probably doomed to eternal conflict. Hell, it might even be biblical prophecy. I don't know.