Also because at this point I think Yoda didn't want to believe that Dooku had completely gone to the darkside. Yoda and Dooku had a sort of bond between them (read Dark Rendezvous) and at this point Yoda didn't want to fight and kill his former apprentice. He admits at the end of AOTC that Dooku is indeed evil, but during the fight Yoda was merely going for a TKO.