Maybe.....I'll give them the benefit of the doubt.
However, the following excerpt is intriguing. It implies that the authors knew that they would be suspected of making common cause with discredited anti Semites. And sought to inoculate themselves from it.
----snip----
The authors attempt to distinguish their argument from that of classical anti-Semites, writing at one point, "there is nothing improper about American Jews and their Christian allies attempting to sway U.S policy towards Israel. The Lobby's activities are not the sort of conspiracy depicted in anti-Semitic tracts like the Protocols of the Elders of Zion." At another point, the authors distance themselves from the president of Iran by writing, "Israel's survival is not in doubt - even if some Islamic extremists make outrageous and unrealistic references to 'wiping it off the map.'"
Most people have motivations for what they say. Whether or not they are conscious of them. It's a cause (motivation) and effect (their words/actions) situation.
My point is that if you only take the words on their merit while ignoring motives you will not fully understand the argument.
With regards to the Harvard paper in question I suspect their motives aren't a knee jerk anti-semitism. I think it's based on fear. Fear of a broad drawn out war in the middle east. If we can dump little Israel and the Jews we can appease "them" and thus remove the threat of a war without end and in the process our fear will be alleviated and we will achieve "peace in our time". i.e. appeasement.
.Why save little Checkoslovokia when we can have "Peace in our time"