Everywhere I see people complaining about that last holorecord. I still don't see how anything has changed, apart from the fact that Bastila wasn't with Revan when he fought Malak and that Revan suddenly seems to be taller.
But the fact that they met the Sith baddie in wild space was just filling in a missing plot point. They never did explain why they suddenly returned as Sith.
Also, people seem to say that TOR just completely forgets Kreia's rants in KOTOR 2, but it actually is possible that Revan was still trying to prepare the Republic for the Sith invasion.