I don't think the argument is whether or not commoners should be able to attack at all, but whether they should be able to do so as well as a first level fighter or rogue. Conversely, the question can be phrased: "Should Fighters and Rogues have combat abilities/stunts that commoners don't."
Guns are far easier to use than primitive handweapons...that's why they end the reign of aristocratic warrior classes, historically. Modern crossbows have "learned a lot" from guns and are far more sophisticated and easy to use than their medieval counterparts. That said, I suspect that a peasant could probably fire a crossbow that he found on a table, but would run into difficulty attempting to reload it. (Although crossbows took far less training to use than longbows.)
Of course, two commoners can kill each other...I don't think people are arguing that commoners couldn't make basic attacks. I mean the dude and the intruder are probably both d6 hp commoners (to use 3e terms.) So the one guy got lucky and rolled max damage (maybe critted?) and other guy rolled low hp. Or maybe the fight took more than one round. Tada, one commoner killed another. What people are suggesting is that neither one of them did anything particularly fancy during that fight.
Okay. You both probably still have single digit hp (again in 3e terms.) HP are abstract (sadly, perhaps). So if this guy had 4 HP and you did 4....he's incapacitated.
I'm not sure about the magic stuff. That varies a lot in the genre. In some of my favorite fantasy sources, there are no gods (or at least they don't seem to be any evident than they are in this world) and priestly casters are just wizards with credentials from a church. In other sources, magic isn't just a matter of training, its a special thing that only some few chosen people get to do ever. Sometimes I don't like how D&D (and many rpgs) treat magic as if its just an alternative to science. That always leaves me thinking about Magitech.
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In any case, both are probably something that should be set up to vary between campaigns and playgroups, rather than firmly fixed in the rules.
I am not saying they should be as good as a fighter. But they might be good enough to kill some Kobolds.
As for the magic/cleric thing it should of course be up to the DM and the flavor of his game.
But a mob of commoners with pitchforks ought to be a risk for low level characters. A pitchfork through your lungs can ruin anyone's day.