The controversy around his dissertation prevented him from obtaining a position at a North American university. He continued as a private scholar while working as a high-school teacher, janitor, and house painter until he was awarded a guest professorship at the École Biblique in Jerusalem in 1984. This appointment proved controversial among Israelis, who, according to Thompson, objected to his earlier study casting doubt on the historicity of the Jewish origin narratives. He then worked on a project on Palestinian place names for UNESCO, criticizing Israeli authorities for de-Arabicizing Palestinian place names. Accusations of antisemitism led to the project being closed.