>Dhimmi status is bad!
Except that doesn't seem to the be the case in the context of the time for specifically the Jewish communities living in Muslim-controlled regions? Per https://en.wikipedia.org/wiki/Dhimmi - "Generally, the Jewish people were allowed to practice their religion and live according to the laws and scriptures of their community. Furthermore, the restrictions to which they were subject were social and symbolic rather than tangible and practical in character. That is to say, these regulations served to define the relationship between the two communities, and not to oppress the Jewish population." There's a section on Jews on that page that seems unanimous in the view that while dhimmi status was not as good as being a muslim citizen, it was a better than what they had either before the Muslims took over or what they had available elsewhere. It's weird to label what is generally an improvement in living conditions/social regard as stemming from deep-seated discrimination.
Per atrocities - of course there were atrocities committed against Jews. Just as there were atrocities committed by basically every long-lived group against every long-lived group in their territories. No one is stupid enough to say that Muslims have never persecuted Jews, just as they wouldn't say that Christians have never persecuted Jews, or that Muslims never persecuted Christians, or that Christians never persecuted Muslims, or that those groups never persecuted themselves in schisms and internicine warfare. But the impression that Islam is fundamentally and necessarily opposed to the practice of the Jewish faith is fairly contradicted by even the history of dhimma. As the first paragraph of that Wikipedia page states; 'Dhimmī... is a historical term for non-Muslims living in an Islamic state with legal protection. The word literally means "protected person", referring to the state's obligation under sharia to protect the individual's life, property, as well as freedom of religion, in exchange for loyalty to the state and payment of the jizya tax, in contrast to the zakat, or obligatory alms, paid by the Muslim subjects. Dhimmi were exempt from certain duties assigned specifically to Muslims if they paid the poll tax (jizya) but were otherwise equal under the laws of property, contract, and obligation.'
On the other hand, look at how the Jews were treated during the Islamic Golden Age in Spain; https://en.wikipedia.org/wiki/Golden_age_of_Jewish_culture_i... ("The golden age of Jewish culture in Spain, which coincided with the Middle Ages in Europe, was a period of Muslim rule during which, intermittently, Jews were generally accepted in society and Jewish religious, cultural, and economic life flourished."). It's hard to square that with the idea that there is this deep-seated hatred among Muslims towards Jews as the GP stated.
My point is that conflict between the two sides is not inevitable, nor is this idea of extreme latent anti-Jewish sentiment in the Muslim world really true. Purges and persecution that people bring up are probably not caused by ancestral hatred, but rather the same thing that causes every society to suddenly fall into itself in violence and accusation; uncertain economic conditions, unstable political environments, natural disaster, epidemics, war, idiotic rulership, etc.