I have exactly the same requirement - I want modules to be able to use a view-discovery like mechanism to specify what types should be used when creating views for a given region and we also want certain regions (or region managers) to use child unity containers to allow us to inject specific dependencies for those scoped regions. View injection won't work as at the point where the module is initialised these regions have not yet been created and using the region context is cumbersome in comparison - to start with it requires that each region be individually tagged with the appropriate unity container.
My solution was to extend Prism and replace the view discovery mechanism with one that searches the logical tree for a scoped injection container which is then used to resolve the view (rather than using the globally scoped injection container). I've hosted the source code here
http://code.google.com/p/container-scoped-prism-regions/
Its not perfect but it seems to work well enough.