Because he was saving the Chosen One.
Or maybe for the same reason Obi-Wan didn't kill Vader in ROTS. In both cases the Jedi did not kill the Sith because the Sith used to be the Jedi's Padawan.
I doibt Yoda would have wanted to kill Dooku anyway. I think he was just trying to capture him. Otherwise I think Dooku would have already lost before then.
yoda had a choice:
-kill dooku
or
-save anakin and obiwan
he chose to save the jedi. its painfully obvious that he needed to focus all his attention and energy on levitating the column in order to do that. which dooku knew and that was the whole point of him knocking it over in the first place.
can this issue die now?