Imma be honest, I kinda suspected this. I wanted Baki to actually "Do it" but he's not that kind of person. Plus seeing as Musashi is Japanese, I don't think the Japanese Audience would've taken having a historical figure be murdered in one of the most popular Manga in Japan (Apparently Baki's way more popular in Japan than in America, but that's because Itagaki has refused to have his Manga translated to english several times. either it's that or the other rumor that it costs a ton, and the western audience isn't big enough to justify it yet.).
BUT, I CALL BULL We've Got Assassin's Creed which made George Washington, our First President a Villain. Baki probably wasn't going to kill him, but this was in no way a defeat. I could understand the over-complicated ending of Baki Hanma, but this was hyped up too much!