Greleag:
Villagers base their enemy response (ie the thing where they attack and refuse to accept commodities from enemies) off of enemy status with the village itself. They don't care if you're enemied to the org that controls the village, as long as you're not enemied to the village itself.

There is one exception (which is probably intentional): village commodity shops refuse to sell to you if you're enemied to either village or controlling organization. I'm not sure if village stables also follow this exception or not.

foolofsound:

The problem being that having guards attack you as you try to do commodity quests (for Commercial) makes them difficult or impossible, thus making Commercial non-viable.

The same thing can be said for Religious. You can't sneak into a village and influence if there are guards hounding around. In fact, it's even worse for Religious than Commercial - for the former you have to stay in the village to influence for a longer amount of time as opposed to the latter, where you can just zip in, give x to y for the quest, and pop out.

The whole village feelings system seems to be predicated on the idea that most people can get into most villages, and the instances of guards-and-statues-and-enemying are the exception used to address the few who go in to kill everything. The same attitude applies to a lot of things in Lusternia: the way the villages are cited as midbie influencing grounds and quest destinations, for instance, and the way the tradeskills are balanced around commodity production in villages. It's like some parts of Lusternia are still running on 1997 concepts and no one's willing to either adapt them to how things have become, or to take steps to change things back to where these kinds of assumptions are still valid.

Lendren:

There is one exception (which is probably intentional): village commodity shops refuse to sell to you if you're enemied to either village or controlling organization. I'm not sure if village stables also follow this exception or not.

No, amnesty lets you buy from comm shops. I've gotten amnesty for that reason alone a few times.