SharePoint does not rely on the O/S for file permissions. SharePoint content is stored as BLOBS in MSSQL databases.
Reassigning ownership can be done for a fairly large number of files very quickly (by a site collection administrator) but apparently the number here chokes the web interface. Wouldn't be the first time.
The command-line utility for SharePoint does not, AFAIK, include an operation to assign ownership of files or list items. (UPDATE) There are many other things I've used it for in qx//, but this isn't there.(/UPDATE)
girarde has been administering two large SharePoint farms fulltime for about a year and a half, and was running farms and/or bits and pieces of them since 2004.