There is no support in Alfresco for storing sites in different / multi-level folders independent of the default Sites folder with its flat hierarchy. There might be a technical way to achieve something like what you outlined, but it would involve circumventing some of the core automatisms / guards that protect sites. It is technically possible to move a site from the Sites folder into an arbitrary structure within the Repository and modify permission setup / inheritance to use that structure for default visibility inheritance (instead of the default "visible for all"), and use secondary child associations to link the site back into the Sites folder so that all default functionality works without a problem (e.g. Share UI / dashboard configuration). I have never tried myself and would not really recommend it, but from other customisations I have done in the past, I am perfectly certain it would be feasible.