I was thinking that, in order to prevent such a thing, however much rep you gain with a faction, it goes just as far negative if you leave. I've never switched beyond the initial switch from TL to Icarus when all reps were zero, so I don't know how it currently works.
atm when you leave a faction that faction goes to 0
and goes into minus numbers for every job you do with your new faction
and like you said you have to work through all the negative rep you have with your new faction before they start giving you points again.
someone suggested its easier to stay in the old faction and store up a shedload of points ready to take with you so you have some to spend to even the playing field of whatever new faction you join.