I'm thinking the same as the Doctor, and had always assumed that Taris fell under Sith control only after the Space Battle that took place at the beginning. And the power and gov't transferring all happened while Revan was unconscious for the past few days, giving them time to prepare.
This was the reason why they declared Martial Law and later destroyed the planet, to search for Bastila and Co. and then later prevent them from escaping.
Also, when the opening crawl states "In the skies above the Outer Rim world of Taris.....", why would they attempt to halt the Sith's domination above Taris at that point in time, being that they were ambushed?
Plus it doesn't specifically say where the ship was heading beforehand, just that they engaged in a battle (presumably because of the ambush), and the Jedi decided to try and stop them right then and there.