I've heard of the Red Jews; however, I'm not familiar with them, so I really don't know what is different about your story. In any case, I can still address your question.
The way you use it isn't expressively anti-Semitic, so in that regard they are fine. You make sure to not describe them as a people as evil or malevolent. If you described them as horrible people as a whole, then it might qualify for anti-Semitic labels; however, you note "that is simply not ture and ignorant" to European claims, and provide what they are really like. Is the description after it bad? No, so that alone is not anti-Semitic.
As for the radicals, they are the outsiders and outliers of that society; therefore, they don't represent the whole. It would be like applying Lenin to all Russians, which would be a mistaken. Not all Jews are good, so it is possible to have a Jewish villain. Just, don't make all the Jews villains, and you escape anti-Semitic labels, rightfully.
So, basically, you are in no way anti-Semitic: You describe the Jews warmly, noting a few Jews who happen to not be very nice. You give a historical background, noting the different views, so I'd say you are doing a historically accurate and great job.
@ Rainbow - Considering that I'm a counter example, RIGHT ABOVE YOU, I'd say that's just silly. I fully recognize that some might not see Jews as the Chosen People. As long as you don't believe that, because I'm a Jew, I'm something worth less or something negative, then it's not anti-Semitic.
