I’m a little confused here, so forgive me if I’m misunderstanding. This topic you’re linking to doesn’t have anything to do with Akita. The entire point there is that the person is not using a theme that is setup properly for sidebars. They’re using a theme from who knows where. None of my themes would have that issue.
Akita and the news scroller plugin should work fine together, and you shouldn’t need to customize anything. You can see them working together here on the live demo: http://www.themeblvd.com/demo/akita/ — Here is the most recent version of News Scroller plugin, Akita theme, and WordPress.
Maybe you could link me to your site where you’re having the issue?