I don't think it's very silly to ask the question of why these NPC classes exist. They are so bad that even the writers tend to ignore their intended purpose (mook jobs) in writing - hence the surprising number of low-level Fighters guarding walls and manning outposts and taking those jobs from the poor Warriors. You'll notice that the NPC classes are largely ignored and relative abundance of low level main classes assumed in the sourcebooks (Complete Warrior, for example, assumes lots of low-level Fighters in its magical warfare section). Eberron created an entirely new, pretty useful, NPC class because the existing ones don't even fit in the theme of standard D&D tropes, and ignores even that class a lot of the time
I hope that, if they still exist in 4e, they are cut down to at most 5 levels and given a modicum of a reason to exist (backbreaking Commoner labor doesn't even rate a good Fort save? Even those wimpy wizards who have never seen a callus or suffered the sniffles are tougher). As is they are just fodder for joke characters (level 20 commoner with skill focus (basketweaving), etc). Really there could be a single 5-level "Non-Player Class" that could replace all of the existing ones without a lot of work, assuming you want to keep the main classes out of reach of non-heroic individuals.
The only truly good thing the current system did was eliminate the lame 0-level NPCs from AD&D.
* I'm intrigued by this Dragon article that was mentioned, what issue was it in?
* Allowing Commoners/NPCs to "trade in" levels also is a cool idea (and at least gives a reason to run a "prequel" campaign where farmhands and the village herbalist find their destiny). I'll be stealing that and the xp for housechores idea in the future I'm sure for any "from the dirt" campaigns even if I don't use the NPC classes as presented.
Thanks for your commentary.