I am currently a student at Ben Gurion. I thought I would add a few of my thoughts on this matter. First of all, we have had students of palestinian descent complete our program. While I am certain they faced some challenges that other students did not, the overall culture of the school was one of acceptance. There were a few religious or nationalistic people that found it reprehensible to have the "enemy" in the classroom with them, but this was a solid, quiet, minority. The administration is supportive of a diverse student body, thus, I doubt you would have problems with any of the other students. The larger problem came when travelling in and out of the borders of Israel. It can be quite a headache dealing with security, but it is something that you get used to and can be overcome.
Currently we have muslim students studying in the program (as well as christian, mormon, jewish, etc...) . While I cannot speak for them, they certainly do not seem to be marginalized due to their beliefs. The truth is that we are a very diverse student body with a strong common interest in international and third world medicine. Coming from very different backgrounds, we often see the world , and events, in different shades (or even colors). Our political views range from far left to far right with most being in the middle somewhere. At times, we have political discussions that became heated as it is sometimes impossible to understand anothers beliefs. I think it has been a great learning opportunity to be exposed to diverse beliefs, even if it is difficult at times (of course, they are all wrong and I am right). And, despite our sometimes lively debates, at the end of the day we try to leave all of our differences behind and grab a beer together.
If you are interested in international medicine, perhaps you should consider applying to our program. If you aren't, perhaps Sackler or american schools would be better suited for you..