Quran 66:9 – “O Prophet! Strive against the disbelievers and the hypocrites, and be stern with them. Hell will be their home, a hapless journey’s end.”
The above passage says nothing about killing, it just says ‘strive against’. Strive can simply be living one’s own life as a firm believer in Islam and not giving into non-believers. It says nothing about war or to kill. Even if the above passage was about war, it would still be subject to the other passages where Allah makes it clear, only when they attack first, are the Muslims in self-defence are allowed to fight back.
Muhammad Asad commentary
20 See note 101 on 9:73, which is identical with the above verse.
101 I.e., ‘do not compromise with them in matters of principle’. Regarding the meaning of the verb jahada (‘he strove hard’, i.e., in a righteous cause), see surah 4, note 122. The imperative
122 The term should Mujahid is derived from the verb jahada, which means ‘he struggled’ or ‘strove hard’ or ‘exerted himself’, namely, in a good cause and against evil. Consequently, jihad denotes ‘striving in the cause of God’ in the widest sense of this expression: that is to say, it applies not merely to physical warfare (qital) but to any righteous struggle in the moral sense as well, thus, for instance, the Prophet described man’s struggle against his own passions and weaknesses (jihad an-nafs) as the ‘greatest jihad’ (bayhaqi, on the authority of Jabir ibn Abd’Allah). 
Mualana Muhammad Ali
9a. The verb translated ‘strive’ is jahid, from which is derived the word Jihad, and the context shows that by striving is not meant the carrying of a war, for war was never proclaimed against the hypocrites, who, in fact, were all practical purposes treated as Muslims. Therefore, when the Prophet is commanded to carry on a Jihad against the disbelievers and the hypocrites, it is clear that Jihad is something else than mere fighting. 
 The Message of The Quran translated and explained by Muhammad Asad page 1188
 The Holy Quran Arabic Text with English Translation, Commentary and comprehensive Introduction [Year 2002 Edition] by Maulana Muhammad Ali page 1109