Further the earlier discussion about the Sith Pirates, it could just be a matter of perspective too.
There is a group that is engaged in combat with ships and to some they are seen as pirates to others they may be seen as a legitimate military force (just as some groups are labelled terrorists or freedom fighters in the news today depending on which part of the world you watch it from). The Jedi may be viewed in the same manner.
As for Anakin's fall it could be more like Kagemusa, Anakin kills the previous Darth Vader and adopts the role with good intentions (using them as a force of good) but the power goes to his head, the role possesses him until he becomes the person he killed.
This could be hinted at by having Anakin discuss the possibilty of using them as a positive force before he vanishes and is presumed dead.
Another character which could give an interesting alternate origin of Anakin could be Kasper Hauser http://en.wikipedia.org/wiki/Kaspar_Hauser
A boy with no past who has been locked away for all his life and is sent to Obi-Wan to be trained as a Jedi because a note claims his father was a Jedi.
As he is trained his memories begin to return and they could form the basis of his eventual fall.