Not 100% sure on this since I'm not familiar with Eclipse update site building, but this page: 
http://wiki.eclipse.org/Equinox_p2_Metadata_Generator
Seems to indicate you can generate the metadata for the update site using org.eclipse.equinox.p2.metadata.generator.EclipseGenerator which includes the site name as a parameter: 
  Arguments describing the output
  
  [...] 
  
  -metadataRepositoryName
  
  a user friendly name for the metadata repository
Perhaps that's what you need, to generate the metadata for the site? See http://wiki.eclipse.org/WTP/What_we_have_learned_(to_love)_about_P2 as well: 
  ...Since you have both a content.jar and a site.xml at that location, you 
  actually have two repositories. You have a classic update site, and a p2
  repository (these files don't know/care about each other).  Classic update 
  sites don't contain a site name (site.xml has no name element), so these 
  sites are "nameless". p2 repositories contain a name element so they have 
  a human-readable name.