On using "apartheid" in the Israeli context

I am grappling with this question/article by Akiva Eldar - Are Israel and apartheid South Africa really different? Eldar claims, “In Israel, ..., institutional discrimination is meant to preserve the supremacy of a group of Jewish settlers over Palestinian Arabs. As far as discriminatory practices are concerned, it's hard to find differences between white rule in South Africa and Israeli rule in the territories; for example, separate areas and separate laws for Jews and Palestinians.” I think that there are two issues being conflated here; the issue of discrimination in the West Bank and the use of the term “apartheid.” I will address the latter first.
Apartheid is a Dutch word for separation. Everyone knows that it is a reference to unjust and discriminatory White rule in South Africa. Some people use the term because they want to compare the injustices of the Apartheid regime in South Africa to those in the occupied West Bank. (In Israeli politics, everything is up for scrutiny, including the adjective I just used for the West Bank, but I will stick with it as even the former right wing prime minister, Ariel Sharon, has used the same adjective to describe Israel’s presence in what some call Judea and Samaria.) The question is whether the use of the term is helpful in addressing the questions Eldar has about Israel’s behavior vis a vis the indigenous Palestinian population.
For me, it is a no brainer that Palestinians, who are not autonomous in the West Bank and are patrolled by the Israeli military are subject to discriminatory practices. They have different license plates, drive on different roads and have different levels of representation with regard to the authorities that control their political destiny. Israelis in the West Bank are full citizens of Israel while Palestinians are not. The social and economic conditions for Palestinians and Israelis are completely different. The respect for human rights is different toward Palestinians than it is for Israelis. But I am not looking to equalize the status of Israelis and Palestinians. I want two states for two peoples. Let the Palestinians rule themselves. This is even the stated goal of my Israeli prime minister.
So what about the word “apartheid.” Are people using it because it describes the separation we “officially” (in the sense that it is the policy of our government) aspire to? Or is it being used to infuriate and paint Israel as a degenerate nation?
I think that people like Akiva Eldar are trying to force Israel to look in the deep dark truthful mirror and decide whether we are really working toward separation as two distinct nations or whether we are comfortable living with this ugly status quo. I have great respect for his efforts, even if I question his method. I don’t think Israel is an apartheid nation. Many of her behaviors vis a vis the Palestinians look and smell like... But, ultimately, using this term is not advancing the effort to change the status quo, so I am joining the chorus of those who will refrain from its use.
At the same time, I have no interest in regulating how people express themselves, and I am glad there are people out there who are willing to put the mirror in our faces. After all, we need to remember that we describe ourselves this way.
“The State of Israel ... will foster the development of the country for the benefit of all its inhabitants; it will be based on freedom, justice and peace as envisaged by the prophets of Israel; it will ensure complete equality of social and political rights to all its inhabitants irrespective of religion, race or sex; it will guarantee freedom of religion, conscience, language, education and culture; it will safeguard the Holy Places of all religions; and it will be faithful to the principles of the Charter of the United Nations.”
With this as our creed, maybe we who care about changing the status quo should replace “apartheid” with “Jim Crow” since Brown vs Board of Education pointed out about these laws that separate but equal is inherently unequal, just like claiming the desire for two states for two nations while continuing to occupy and oppress Palestinians is inherently dishonest. Of course, I know what will happen. Those who want to drag their feet, our nations feet, will draw attention to the use of the “inappropriate” comparison and distract us from the business of getting back to our professed national goals of “freedom, justice and peace as envisaged by the prophets of Israel.” Ultimately, this is the most important objective. The rest is just words.