To change favicon you need edit lib/perl5/site_perl/5.8.8/IkiWiki/Plugin/favicon.pm and change line
    $template->param(favicon => "favicon.ico"); 
at the end of file
And rebuild wiki:
  ikiwiki -setup your_wiki_config
After reload page you'll see your new favicon.

That method allow configure Animated PNG even:
ikiwiki.sphynkx.org.ua