i don't know about the whole "having a master" thing
sure, maybe it could explain away some of the earlier levels (master teaching you the ways of the force blah blah)
but am i the only one that thinks killing them off like most people are suggesting is kinda... lame?
i was pondering an idea where you were a padawan, had a master etc. slowly learning the force through some intro sorta missions with said master, then after a while, learning about some big magical motivation to take off to the unknown regions to help/hinder Revan and the Exile (i don't know, maybe the Exile is your uncle's-best friend's-sister's-husband's-former roommate or something)
at this point you would still be fairly neutral, and in exploring the unknown regions, sorta guide your own path, following the jedi code or not, as you choose to
in the end, fight the inevitable big bad boss and return home to the jedi, and if you're dark sided, try and take them on (maybe fighting your old master as a post boss-fight boss), or if you're light sided, try to fit back in to your old place in the order (maybe being exiled for your actions ala the Exile after the Mandalorian Wars, or the Vault Dweller in Fallout 1)