I know you can get yourself "expelled" from a faction, but is there any way to keep the faction from appearing on your 'list of joined factions' in the character menu? I know its lame, but my thief is regretting having joined the fighter's and mage's guild (not to mention the fact that it makes the faction list look ridiculously long) and I was wondering if there's any way--mod, console or otherwise--to make it as if I'd never joined?

The only way is http://www.uesp.net/wiki/Tes3Mod:PCExpell, but that is same as "I know you can get yourself "expelled" from a faction". Sry, but I think you are stuck...

I checked to make sure lowering your rank can remove you the way raising you in a faction you don't belong to will add you, and it doesn't seem to work. So there doesn't seem to be any way.

A thread asking this question was asked just the other day and in that thread it was established that it's impossible to leave factions, only to be expelled or pretend you've left.