I really don't see what the problem here is. Yoda is a Jedi.
FACTS:
1. Jedi are mammals.
2. Jedi fight ALL the time.
3. The purpose of the Jedi is to flip out and kill people.
Honestly. though - the day after it came out that scene is all anyone talked about. They even made the post-release advertising center around it because they figured that would get more people to go see it.
I remember this guy at work freaking out about it and giving us every detail. When asked about the rest of the movie, he just shrugged, said it was okay, and then told us AGAIN how the Yoda/Dooku scene played out.
I thought the scene was decent, but had seen enough footage in the ads and heard about it so much that it wasn't a surprise for me. The crowd at my theater went crazy and started clapping during the whole thing.