@tubbyc: I'll start with the definition of 'innocence'. In the most purest sense of the word, only Prophets and angels can be innocent. As for innocence in the context of who shouldn't be killed, it includes just about anyone (Muslim or non-Muslim) except for three kinds of people:
1. The enemy in war.
2. Those who commit Hudd crimes. (specific ones; it follows proper trial and is a long subject)
3. Those who commit some types of Harb crimes - terrorism, rape, etc. Again, proper trial is followed and complied with.
Were we to say that Quran is to interpreted through Muhammad's (pbuh) life then we would be contradicting our own selves when we try to justify that Quran wants Muslims to kill non-Muslims simply because Shirk is worse than killing; because Muhammad (pbuh) didn't do that except for the 3 conditions I've written above. I find it worth mentioning, a quote of Ali ibn Abi Talib (R.A), the Fourth Caliph of Islam:
"Remember, Maalik, that amongst your subjects there are two kinds of people: those who have the same religion as you have; they are brothers to you, and those who have religions other than that of yours, they are human beings like you. Men of either category suffer from the same weaknesses and disabilities that human beings are inclined to, they commit sins, indulge in vices either intentionally or foolishly and unintentionally without realizing the enormity of their deeds. Let your mercy and compassion come to their rescue and help in the same way and to the same extent that you expect Allah to show mercy and forgiveness to you".
Letter 53 - To Malik Al Ashtor for Governance
Another worth mentioning quote of Umar (R.A), the second Caliph: "I wish there was a wall of fire between us and the Romans. So that neither can we cross into their lands, nor they in ours''.
The article you posted commits this mistake: it starts off by accepting that Muhammad (pbuh) life is to be taken in account while interpreting the Quran and then it deliberately ignores his life for the rest of the article to justify whatever it wanted to justify. What Muhammad and the Quran mean by saying that, ''fight until there is no more fitnah'', is simply, deeply, that as long as there are people who commit fitnah (rebellion also counts; even of Muslims against Muslims) then there will be war. Imagine there were only Muslims in the world, then there would be only one sort of 'war' left: Civil war. Other than that, there would be no more reason given to you to fight. Another Hadith I should quote from Sahih-al-Muslim: "O believers! say that we don't wish to fight. But if fighting is brought upon us, then we stand steadfast''. What I'll suggest you here is that, before jumping into the Quran or the depths of Islam - that's someplace where 95% of even the Muslims of this age haven't jumped - you should read about the people who upheld this religion; the people who are unanimously deemed as the 'true followers of Islam'. That is, Muhammad (pbuh) and the Rashidun Caliphs. I don't think you'll find anything veracious about Muhammad (pbuh) on the internet but Tariq Ramadan's book "In the footsteps of Muhammad (pbuh)", is the best thing you can get if you're looking to know about Muhammad (pbuh) AND his teachings. As for the Rashidun, just reading their wikis will suffice, for now.
You have to understand that the worst sides of Islam have only been brought up 1400 years after the religion's advent. That ought to raise some suspicions. One thing that even us non-Muqallid Muslims do is that we adhere to whatever Muhammad (pbuh) and his followers did. Whatever political conspiracies happened afterwards had nothing to do with Islam. And whatever divides occurred afterwards, again, had nothing to do with the religion. Simply put, Muhammad (pbuh) said this, "There will be 73 sects in my Ummah, and not a single one of them will go to heaven save for one: those who'll follow me and my companions''. That is all. I hope I was of help.
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