According to Wookieepedia on all the class characters, all republic characters are lightsided and all Sith Empire characters are darksided. I take this to mean that the flashpoints would also represent that.
That was just the general consensus so they could write down the stories to provide the expected information.
As for Revan...yeah, BW basically left this open. If they ever need a boss for an operation or something, they have Revan. If they ever need a Force Ghost, they have Revan. All options for the writing department. But the truth will be revealed...eventually.