Rather than "banning" an entire site that seems to have some spammy pages, why not index only the home page, and flag it in the Google Webmaster Tools dashboard

Rather than "banning" an entire site that seems to have some spammy pages, why not index only the home page, and flag it in the Google Webmaster Tools dashboard? Also: are any specific notices or warnings given in Google Webmaster Tools, to inform the webmaster and give some clues about the findings and decisions of your team? Thanks Matt for taking time to explain things here.