To get faction points in space you have to go to a faction station and declare your self to your chossen faction, then you can gain faction points for killing opposing factions, but be warned this opens you up to being killed by other overt players in space.
As with all pilot trees you will be connected to some faction at some point, this will mean you can't shoot at this faction (like shooting a pc ship you get that annoying noice) and i know some of them change aliances as you progress.
I think for freelance that faction is all dependent on where you start. I know i starting on tat can't shoot hutts, but can shoot either rebs or imps, but on another account where i started on corro i couldn't shoot ties :(
But as i have neve been an imp pilot and am a rebel sympathetic freelance pilot i dont know about getting imp missions.
One last word though, i dont know if this has been rectified yet as i am not yet a master of either of my choosen factions (mainly do you lazyness on my behalf,) but as a master freelance pilot i don't think you can get in to deep space