Regardless of whether or not their content is good or evil, these paintings are a form of historical documentation. They could be removed form areas that tend to promote their content, such as churches, but they should not be destroyed. They should be viewable in areas that address them in context, such as in a museum with a display on anti-semitism, or in a Holocaust museum. That's the general idea. We should no more destroy art like this than we should Nazi propaganda. Both must be retained for historical knowledge. We humans generally fail to learn from the past, but we must preserve these items if we hope to.
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from the article: Pro-Israel group asks Pope to remove anti-Semitism from religious art