Nice
I like the idea of a ninja facing off with a jedi/sith. However, I don't believe that ninjas can't be affected with the Force. They're using the Force but just have a different understanding of it. Just like Jen'saarai, White Current users, Force witches, and many more in the Star Wars EU who have a different understanding and use of the force.
You should try facing off Galen Marek (Darth Vader's secret apprentice) with a ninja. Now THAT would be nice.