One thing to point out about the guns is that if you look at the studies comparing gun prevalence and homicide, you find that gun prevalence specifically correlates with gun homicide, with no significant effect on non-gun homicide. So this strongly indicates that there is an instrumentality effect: that guns actually cause, or at least facilitate murders. If it were actually the case that the guns/homicide correlation were due to a common correlation with low social capital, you'd expect to find a correlation between guns and all kinds of homicides, not just gun homicides.
In fact, a likely interpretation of this data is that gun prevalence is one of the ways that the social capital causes more homicide (at least partially so). In other words, when social capital is low, people go out and buy more guns, and when people have more guns, they end up committing more homicide.
This is also consistent with what social scientists have observed in other studies of gun crimes. Most homicides result from either escalating conflicts or other crimes (e.g. robbery, assault), but since gun assaults are much more lethal than assaults with other weapons, the presence of a gun makes it far more likely that these other situations result in an actual homicide rather than just an injury. And this explains, for example, why the US has comparable overall violent crime statistics to other industrialized nations, but we have far more homicides -- it's because criminals in the US have a much easier time getting guns.
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