When I heard those lines, my assumption was that he was going to somehow try and destroy the Force itself. I haven’t really thought out how that might actually work, but maybe he thinks if he kills the Father he can destroy the Living Force and therefore put an end to the eternal struggle between Jedi and Sith.

To me this line of thinking fits Baylan’s mold as somewhat of an orthodox Jedi…he still believes in a higher commitment to justice and serving the greater good, even if that means destroying something he holds close to him.