It appears you may have the 'sysadmin' role applied to your SDE user. You can revoke this in SQL Server Management Studio by going to the Security folder > Logins> right-click on the SDE user > Properties > Server Roles. Uncheck 'sysadmin'.
I just had this issue and that solution didn't work for me - I got a "not enough permissions" type error. But I followed the solution here: http://support.esri.com/en/knowledgebase/techarticles/detail/40606
And simply re-connected to the geodatabase I wanted to enable with my "sa" user instead of "sde" and ran the "Enable Enterprise Geodatabase" Tool, and that worked. So you might try that alternative if someone comes across this thread.