I admittedly have not read the book you referenced, but this seems to be a pretty irresponsible representation of the Qur'an and, more importantly, a pretty weak argument. I'm not suggesting that things have not been interpreted the way you state, but a very cursory examination of the context of those scriptural citations suggests very selective quoting.
The Jews are likewise marked for destruction. Islam's long history of anti-semitism finds full expression in the Koran. Jews are described as being made into apes and swine.(5:60,2:65, 7:166) They are eternally cursed. 2:61,3:112)
For instance, immediately following 2:61, 2:62 explains that:
"Lo! those who believe (in that which is revealed unto thee, Muhammad), and those who are Jews, and Christians, and Sabaeans--whoever believeth in Allah and the Last Day and doeth right--surely their reward is with their Lord, and there shall no fear come upon them, neither shall they grieve."
Similarly, immediately following 3:112
"They [Jews/Christians] are not all alike. Of the People of the Book, there is a staunch community who recite the revelations Allah in the night season, falling prostrate (before Him)."
"They believe in Allah and the Last Day, and enjoin right conduct and forbid indecency, and vie one with another in good works. They are of the righteous."
In the context of the references to the unbelievers, this is shown and generally interpreted to be pagans, atheists, or Jews and Christians who do not really believe in God. That said, some Jews, primarily the ones who wrongfully killed God's prophets are said to have been damned.