As of now, Muse publishes all html pages to the root folder irrespective of their position and nesting in the Site Plan. I would encourage you to submit that as a feature request to the Ideas section of this forum at http://forums.adobe.com/community/muse/ideas
Posted your suggestion in Ideas.
Would it work to create a separate or second site in muse, thereby placing the pages in a secondary-tier folder, and linking to the pages from the menus in the homepage in the the root folder? Hope that makes sense.
Yes Drew, that is possible. You can publish the subsite to a folder within the main folder. Then attach them to the main site using relative links i.e. /sub/filename.html.