So if you decide to join the vampires in the new dlc and you haven't say started the companions quest could you even get into Whiterun to start it, or would you have to lay waste to the town first because the people will attack you on sight. Has anyone heard anything about this?

I'm pretty sure that only vampires in vampire lord form will be attacked.

Its like a werewolf ability they will only attack you if you change forms into the vamire lord. So your not allways permently in that form but yes if you turn into a vampire lord you will be attacked on sight.