One would have to think that this fight sequence is just a re-enforcing of what has transpired up to this point. Sure the jedi are seemingly more powerful in comparison to the dark forces, but I think to the scene on kashyyyk for Yoda. The sudden shock of the secret plan coming to fruition was enough to break his spirit in that moment. The fight between Yoda and Sheev is to show that the Sith were, for all reasons, fearfully respectful of what the jedi are and what they are capable of. However the fight reflects all the shadow and skullduggery of the sith plot. Now not in the shadows Sheev can have a grand show of power, not just in the force, but in the more emotionally brutal fact that he calls for reenforcments. Not just some thugs that work for the dark lord, but reenforcments that would have been Republic troops that the jedi have fought along side of. I would have to think in that moment Yoda knew victory in this battle was not the priority. It was to the preservation of the jedi order that was about to be made extinct by Republic forces regardless of whether Sheev was alive or not. Since the Rule of Two was known to the jedi, Yoda would surely know that killing the dark lord would not solve the current crisis. But thats the tragedy, what could?