I have multiple sites running WordPress. I have had good luck upgrading through the control panel on most of them.
Last week I upgraded to 3.5.1 on a small site and received the "fatal error" message regarding one of the files in place of the site. Since I couldn't get into the control panel and the site was unimportant, I deleted the site.
Yesterday, I upgraded a client's site and got the same "fatal error" message. I went in via ftp and found multiple WP files that were "0" in size. I downloaded upgraded WP files from another site and uploaded/replaced all "0" files. The site came back online.
Same thing today... another client site... upgrade to 3.5.1... fatal errors. Once I replaced the same "0" files the site came back online.
There obviously is a problem with this upgrade.