I'd agree with Kristian, don't nest your repeater. To get around the issue you're having with the hierarchical viewer, simply add the
MenuItemGroup field to the other page types being used in the viewer. You can hide that field in those other page types but keep in mind it will only get the page types with
%main% in that field so the other page types won't be found if there is no value.
If you're using it specifically for navigation, I'd use a different approach and get rid of that field all together and create a Category called Navigation and add new categorizes below it like Top, Left, Main, Footer, Right, etc. Then assign those categories to the pages you wish to display in the navigation. There is a drawback to this though, in the repeaters and such, you can only select one category.