I don't think that's a very good way to handle it, though. The Dark Side is supposed to be seductive and powerful to even the greatest of the Jedi; if it simply destroyed all their advantages when they embraced it, then the only Dark Side users would be the people who started as Sith.
Just as Anakin Skywalker could become Darth Vader and be powerful in both incarnations, so room must be left for players who want to start out Light and slide into the Dark, or vice versa.
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I think the stronger a Jedi master is the less susceptible he is to the DS. As the name implies he/she is a master of the light side.
I don't understand a player who has already gone the long and hard way to become a Jedi Master and then, without a comprehensible reason, behaves like a schizophrenic maniac. So I don't have any problems with a game that doesn't allow for such strange careers.
By the way, Anakin has never reached the rank of Jedi Master. He's been a young padawan/knight with let me say "mental problems".