<%if Category_Template and Category_Template ne 'navcategory.html'%><%include $Category_Template%><%endparse%><%endif~%>
from your templates anyways since it isn't needed (it was old template code that was left in).
There's currently no easy way to disable the inheritance, but it's on my todo list. In the meantime, You could just use what I suggested above for the upper level categories and clear out the Category_Template values for the categories.
Another thing you could do is create a new column and use that old line of template code at the top of your category.html template:
<%if COLUMNNAME%><%include $COLUMNNAME%><%endparse%><%endif~%>