2:244 And fight in the way of Allah, and know that Allah is Hearing, Knowing. Fight for what? Against who? Simply "fight" does not mean "kill infidels." As I said before, indoubtedly there will be zealots (of all religions) who will INTERPRET that to mean "kill Christians/Jews/Israelis/unmarried girls who show their face in public," etc, but that is not the Koran's fault.
9:29 Fight those who do not believe in Allah, nor in the latter day, nor do they prohibit what Allah and His Apostle have prohibited, nor follow the religion of truth, out of those who have been given the Book, until they pay the tax in acknowledgment of superiority and they are in a state of subjection.
Again: fight does not mean "kill." "Those who have been given the Book" are the Christians and the Jews, and they are obviously exempt. The rest should also be fought until they start diligently paying taxes and mind their own business (which means they should preferrably stay alive and well, so they can work).
47:4 So when you meet in battle those who disbelieve, then smite the necks until when you have overcome them, then make (them) prisoners, and afterwards either set them free as a favor or let them ransom (themselves) until the war terminates. That (shall be so); and if Allah had pleased He would certainly have exacted what is due from them, but that He may try some of you by means of others; and (as for) those who are slain in the way of Allah, He will by no means allow their deeds to perish.
The key words: meet in battle. Also, "make them prisoners" and either "set them free" or "let them ransom themselves" implies they have to be alive.
So, where is the ~chant~ "kill the infidels!" ~chant~ part?