That is precisely why I switched from using MAPI based SQL Agent Mail to xp_smtp_sendmail from http://www.sqldev.net
Once setup, you can bounce the Exchange server as much as you like and email from SQL Server still works.
As for preventive steps. You could try putting together a VBScript of some description to check for running jobs and then stop the Agent.
--------------------
Colt 45 - the original point and click interface