It's going to depend heavily on your class/race.
If your class has invis, then really you don't need to worry about faction at all outside of specific quests you may want to complete.
Those with sneak can sell at any vendor in the world.
The only class that might care about faction is... Warriors until they get invis clicky, and maybe Paladins. But unless you start off an as evil race warrior then you'll be fine in so many cities that ruining a guard faction here and there won't really matter either.
TLDR Faction is pretty much useless, from a practical standpoint.
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