I'm no historian, but the way I see it, if Nobunaga or Shizuko survive the Honnō-ji, the author will have to create new history almost from scratch. If Shizuko survives and eventually starts competing with other nations, the author will probably have to learn more about history beyond Japan's and include it into the story. At that point, is the story still about the Sengoku era? The name of the manga/novel will no longer make sense. At some point, it must end and you really don't want to drag out a story.
Akechi started acting weird when he found out about Shizuko's creating money from nothing idea. He can't just only kill Shizuko, because this is a project that seems to need a lot of involvement from Nobunaga as well. Considering that the author seems to prefer not killing major named characters, sending Shizuko and friends back to modern Japan seems to be the most likely scenario and would fit with the theme of the story. Takeda might be a major character that died, but he was ill anyway and giving him an honorable suicide ritual is one of the better endings from a samurai's pov. Other named characters that died are not that important anyway.
If Nobunaga does end up in modern Japan, he's got to find something to do. There's no war to fight and no one wants to start one, so joining the military is pointless. He could start his own martial arts school, but he does not seem like the type to teach. The only other thing he has experience with is politics. And if he wants to be number one, then he has to become Prime Minister.