Setting permissions on the exe won't work for Enterprise Manager. EM is an MMC snapin.
When setting up your SQL Server ensure that only people that you want to be admins on the SQL Server are members of the sysadmin builtin server role. This includes removing the sysadmin rights to the BUILTIN\Administrators group. Be sure to specifically add your self to the sysadmin's list before revoking the sysadmin rights to the BUILTIN\Administrators group.
You'll also want to be sure to set a Long and Strong password for the sa account. Setup a seperate login for your application to use. Ensure that this account also has a long strong password which is different from the sa password.
Only grant the application account the minimum amount of permissions that it needs in order to function within the guidelines set forth by the applications. For example, if the app never updates a table the application's login should not have update rights to that table.
Ideally all DML should be executed via stored procedures for the maximum amount of security. This way you only grant the rights to execute the stored procedures, and you revoke the rights on the tables them selves. This forces the application to use the stored procedures, and prevents someone who has broken into the server from being able to access the tables.
Denny
MCSA (2003) / MCDBA (SQL 2000)
--Anything is possible. All it takes is a little research. (Me)
(Not quite so old any more.)