
Icyshadow |

They'll die in combat.
Why?
Because NPC classes are horrid, and meant for NPCs. By giving them levels in NPC classes, you prove gameplay-wise (and perhaps story-wise) that they're stuck to the commoner life, unless you later replace their NPC levels with the appropriate proper class levels. Oh, and they are horrid :D

memory |

What's the effect on an AP campaign if I require the PCs to start with an NPC level? My intent is to add flavor to background and have that ordinary people become heroes arc, but I don't know what the mechanical effect would be.
I think it depends on a whole host of factors. How many people are in the group, whether you're going to start at level 1, and how much do your players optimize are all important. So is the ability generation method.
I'm running Carrion Crown for my group now, 4 players, not very optimized, 4d6 drop lowest and they're doing just fine (although luck has played in their favor). I don't know if I'd start them with an NPC level at level 1 and expect them to survive though. If there were 6 of them, or if they optimized seriously or if we did 25 point buy I think it would be fine.
You may want to look into giving them something like a free Skill Focus (profession: whatever) feat instead. Helps give them a bit of a background without changing balance much.
EDIT: Also, I think it's important that you give them Max 1 NPC level if you don't want them to die terribly.

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Let the start as PCs.
For some APs you could start the game by having them play local (non-important) NPCs. Then have some events happen (murders, attacks, whatever). People start dying. Basically, you use this as an introduction to the area. It gets them involved and lets them see it from an NPC perspective instead of a PC party perspective.
Then have them start playing with the regular PCs. Any NPCs that survived the initial attack can be interacted with during the game. Provide information. Be future cohorts. etc.

Anguish |

What happens is you permanently cripple your party by leaving them one level behind where they are expected to be ability-wise. That won't be hugely important to the physical combat types but it will be to casters. They will forever more gain their new spell levels one class level later than the designers anticipated. For sorcerers in particular that's a big deal because they already are one level late, which designers may have accounted for. But two?
Also, think about the healing capacity. First level is already hard enough to struggle through without needing to heal for two days after every adventuring day. Why not make it four or five by taking away actual cleric levels?
It's a good idea flavor-wise but a bad one mechanics-wise. Paizo doesn't pull their punches in APs.

EWHM |
I've seen GMs start their players with one NPC class level and one PC class level. Within a level or two, they're required to convert a level advancement to the change of the NPC class level to a PC class level. So, you might have
warrior-1, fighter-1 who gains a level to warrior-1, fighter-2 who gains a level to fighter-3. Usually the GMs that do that run solo or duo preludes for each character prior to the start of the first 'real' adventure.