Frapple

So I'm travelling through the galaxy, saving all the Jedi I can get my hands on, Landed at Iziz for the first time looking for a way to support the queen & the jedi, studying each conversation but nothing ever arises, so to progress the game I follow the main plot and end up killing some on the other guys men, great I was thinking - I'm now on the side of the queen...turns out they were just a hoax to make it look like I was captured. Story progresses and I'm back on Iziz killing all the queens troops and end having to kill the Jedi & the queen - what the hell! Is there I choice in which side you choose - if so, where did I go wrong? Now I get back to the ship and all of a sudden I'm apparently looking for 'revenge' and 'hunting' the remaining Jedi....what? Anything I can do to get back on track before I land on dantoonine and get stuck there due to -magical plot device 20.7a- and have to kill all the Jedi I saved just to progress the plot and finish the game? Haven't got any save games previous (I tell a lie, I've got one on Peragus) Help!