matrixtooling
If you disable mail on your SME server, then you will no longer receive server generated admin mails, so probably best to leave the SME server mail system functioning.
One answer (perhaps the most obvious) is to reconfigure your email clients & backup scripts & dumb programs to use Google Apps, rather than using the SME server.
If you have reconfigured your email clients and the problem is only to do with the other scripts etc, this may be caused by still having the smtp proxy enabled on SME server. This will force all local mail traffic to go via the SME server. You can disable this in server manager in the Proxy settings panel.
The other possibility is to Delegate mail to another server, that really depends on how Google Apps is setup, I'm not that familiar with it to know whether it acts as a fully featured mail server or not.
See
http://wiki.contribs.org/SME_Server:Documentation:FAQ#Internal_Mail_ServersIn server manager you set the Delegate mail servers address, rather than the SMTP servers Address of Internet provider's mail server.
PS It won't hurt if you do a bit more reading of the manual & FAQs and even explore all the settings in server manager, as my answers above are all documented there.