The "pure canon" differs from the EU on the history of the Sith.
For one, in the Terry Brooks authored "The Phantom Menace" film novelisation (which is higher official level than any EU novel or comic) states that the Sith began as a break-away Jedi sect 2,000 years ago (prior to the events of TPM the movie). The "war" between the Sith sect and the Jedi Order lasted 1,000 years, then they Sith were thought extinct (but in reality, they were simply going with the "only two" rule in hiding). So for 1,000 years the Sith were in hiding until TPM happened.
In AOTC (the movie) we learn that the Republic is roughly 1,000 years old. So the Republic was formed roughly around the time that the "Sith War" ended.
The Jedi Order may be much much older of course, but the age fo the Sith and the age of the Republic pose problems for all the "KOTOR" stories.
So these KOTOR stories might simply be legends (akin to some of the King Arthur or Robin Hood stories, ie: fun, but more fiction than fact), or, (as the EU postulates) some retconning happens like there was a "reforming" of the Republic that started the dating system over and that the "Sith" sect that's 2,000 years old was based on the "lost" rediscovered teachings of some even OLDER sith sect that truly was extinct from thousands of years before or something.
Anyway, it will be interesting to see if Episode III expands any of this, or if it will all be in the EU (I'm guessing the latter).