Maybe houserule a flaw that all noncombatant NPC's have: "Noncombatant: This NPC wasn't made for fighting. Whenever facing a nonanimal monster, or non-npc class intelligent creature, this NPC takes a penalty on saves & attack bonus equal to the opponent's ECL or CR, and, in addition, takes double damage from all their attacks."
With this approach, you can keep all the NPC classes, and amongst them, they work great. A 20th level Commoner still has the BAB of a 10th level fighter - but against that fighter, it's as if he had a BAB of +0. Against a Wizard that level, it's as if he had a -3 penalty on his saves. One power attacked hit and he'd be down, because he takes double damage. Similarly, it explains why big cities don't just give a shortbow for every peasant and take down the dragons that come to plunder them... It's because everyone would just get one-shotted by everything and couldn't even mass up without being wiped out near instantly. Yes, even the higher level ones. Only the town guard would resist a bit more, but they wouldn't have the numbers to deal enough damage to kill the dragon... (only hitting on a 20, most likely, there would have to be hundred's attacking at once to muster the DPS to bring it down, all while the dragon would wipe them out, and flee swiftly if too threatened, probably giving enough time for the adventurers to step in)c
...
With that one flaw, you basically take all the OOMPH out of the noncombatant NPC classes, and so, you could level them side by side with the PC's without wondering why the peasants don't fight back(fear of instant death). Now you can have 20th level commoners, experts, adepts & nobles that could fight the town guard (they don't have the penalties vs NPC classes), but squirm at the thought of even fighting a lvl 1 barbarian... (that could take them down if raging and power attacking because of double damage).
EDIT: of course, that would require another addition: noncombatant NPC's give no experience if killed. That makes them so weak, they can't be worth anything , except as a mob(when you apply the Cityscape Mob template and get a whole different thing, closer to a Swarm).