I think these 'examples that the author provided are misleading....for one, how does the Quran define an "innocent"? The so-called "unbeleivers" in the Quran are not "innocent". As a matter of fact, there is a passage with says that the "unbelievers" are the "vilest of animals" and that Allah would have made them able to see and hear (the word of Allah) except that he didn't 'give' that 'gift' to them because they are evil.
From the Quran:
Surah III
151. For we will cast terror into the hearts of those who disbelieve.
Surah IV
89. If they turn back, seize them and kill them wherever you find them.
Surah V
Do not take the Jews and Christians for friends, they are friends of each other....
Surah IX
5. So when the sacred months have passed away, then slay the idolaters wherever you find them, and take them captives and besiege them and lie in wait for them in every ambush