In response to Athenian's idea of selecting your faction with a new character and then starting out on the appropriate base with proper ID/IFF, I've seen it implemented in other mods so it's definitely possible. The code is already out there and who knows, maybe some other modding team would be nice enough to let us look at it.
Also, to Thexare, we could keep a Freelancer character just that - a freelancer. You start with a Freelancer IFF but you can choose whatever ID you like. Also, you could start out neutral to everybody and your repsheet would be like it is now, completely dependent on who you shoot/take missions for/etc.
I like the idea of a command you can enter after you create your character that will adjust your rep in a certain direction. But if such a command were implemented I believe it should be limited to the Houses and major unlawful factions such as Outcasts, Corsairs and perhaps one or two generic "pirate" repfixes for LR/Xenos/LH/etc. Guard ID/IFF should still take some work, as should various non-house factions like Junkers (not much work really), Zoners, Order, etc.
I DON'T think such a command should automatically tag you, but it should push you close. At least to the point where you can outfit your ship with proper faction equipment.
Just as we reap the golden wheat, must we also cut free of the chains! [eS]