Based on further research I have found that this is a major flaw in the Joomla! routing file.
Normally this will not hurt most sites much, and a simple plugin can usually repair it. However in sites like the one that this question came up from it uses a vast amount of database rows, and adding more to attempt to remedy this will cause speed issues. So basically trading one problem with another. (this is based on over 15 thousand k2 items on none dedicated hardware).
The only solution is to override the normal templates for displaying the views. Instead of using the typical $item->link, you would use JURI::base().'/component/k2/'.$item->alias. This way each item will always fall under the k2 component, and although the url structure is not ideal it will not have duplicate pages.