Well a posthuman couldn't actually have magical powers but their technology would be so advanced, that it might seem like magic to humans. Who's to say that they couldn't develop machines to generate lightning bolts and fireballs or instantly vaporize a city? Also, I'd imagine that they'd be physically enhanced as well as super-intelligent. They would probably have better defences to their brains and hearts then we do.
I don't want to doubt that such technology is possible( sounds like a radio controlled nuke) but you dramatize the effects of enhancements by putting in the ring two fighters, who probably never meet in the way you describe. The impact of the first enhancements will definitely not create true godlike posthumans. The difference between enhanced and unenhanced will more be likely be like the one between the ford t and a horse, thereby giving enhanced people only slight advantages(which nonetheless could make them the new ruling elite). The technology of enhancements will distribute through society at some speed so there won't be giant intellectual gap between the majority and the superenhanced people, but more a situation like we have it today with different IQ's. Maybe enhancements will be socialized so everyone gets them and there will be no more gaps in abilities. Furthermore I don't see why there has to be this one posthuman kills everyone scenario. Why not ten or one hundred posthumans?
On the other hand there will be people who decide to not be enhanced. In the long run they could experience assaults like you describe, which they can't defend against. But this not called a war but a hate crime.
By the way, the idea that there will be individuals who will have the power to decide on the extinction of the whole human race is not a quirk of transhumanistic scenarios. During the cold war we already had this situation( and in some sort of way we still have it today).