Perhaps Dooku knew it was time to leave while Yoda was occupied with the falling column because he had the DS plans on him and he had to get them back to Sidious. And/or Dooku may have been worrying about the chance of Obi Wan somehow getting back into the duel. Highly unlikely, I know - but note after Dooku took off and Yoda Force-pushed the column away from the injured Jedi, Obi Wan didn't seem to have that great a difficulty in getting to his feet, despite his injuries. Anakin was obviously sidelined with the missing arm, but Obi Wan could have been Force-throwing objects at Dooku while he was lying there to help Yoda out.