You cannot see the *Save site  as Template* by default.
We hide the link because we do not support the feature  in the publishing  site.
But we don't forbid accessing to the feature by the link directly, because we allow the 3rd parties developing their own applications using the APIs.

An workaround is using Export command to export the site and import to a Blank template  site.
For more information, please refer to:
l Export: Stsadm operation (Office sharepoint  Server) (technet.microsoft.com/en-us/library/cc262759.aspx)
l Import: Stsadm operation (Office SharePoint Server) (technet.microsoft.com/en-us/library/cc261866.aspx