Then when the Sacred Months have passed then kill the Muushriun wherever you find them and capture them and besige them, and prepare for them each and every ambush. But if they repent and reform As-Salat and give Zakat, the leave their way free. The recompense of those who wage war against Allah and His Messenger and do mischief in the land is only that shall be killed or crucified, or their hands and feet be cut off on the opposite sides, or be exiled from the land. That is their disgrace In this world, and a great torment is theirs in the Hereafter...
Translation...Muslims are instructed to kill all non Muslims no mater the circumstances unless those have converted before those who have convicted them...all non believers must die.