Good post. If I might make a couple points from a historical rather than theological perspective?

It's generally believed by historians that the Quran was compiled after the first rash of conquests - exactly when is open for debate. If you're a devout Muslim, you believe that the Quran is composed of the words of Muhammad, remembered verbatim by his followers and then written down. I don't mean to question anyone's faith, but from a historical standpoint this is unlikely.

So it's a bit of a chicken or the egg thing - are the passages approving of religious war original to Muhammad's teachings (who died after unifying the Arab tribes, but before the expansion out of Arabia began) or were they written in at a later date to justify the conquests? Muhammad almost certainly waged repeated war with neighboring Arab groups in order to unite and convert them. It's certainly the case that medieval Muslims generally interpreted the Quran to be supportive of religious war. This is tied up with the concepts of the House of Islam, that area under the control of the caliphate and the umma, and the House of War, those areas remaining under non-Muslim rulers.

But it's important to note that the pre-Islamic Arabs were quite a warlike group, frequently serving as mercenaries in the Byzantine-Persian wars, or as raiders, both within and without Arabia. It may be that Muhammad incorporated these already extant social features into his new religion intentionally, or that they became melded with it organically after his death. We really don't know, as the first written account of Muhammad's life dates to 120 years after his death. That's farther removed than any one of the Christian gospels, for instance.

Tl;Dr: We don't know a hell of a lot about Muhammad or what he taught due to an almost complete absence of contemporary primary sources.