One method is to create a /scripts/postwwwacct script as described at: http://www.cpanel.net/support/docs/hooks.htm#postwww
Here, you can analyze the name of the package and if it has something like -noemail, you can script the tasks your admins are currently performing manually.
With the domains that creep back into /etc/localdomains, is it possible that they are going to the MX entry editor in the cPanel interface and checking Always accept mail locally even if the primary mx does not point to this server?
There may be a way to create a hook to intercept that as the code that is being executed can be found in /usr/local/cpanel/base/frontend/x3/mail/dosetmx.html:
Code:
<cpanel Email="changemx($FORM{'domain'},$FORM{'mx'},$FORM{'priority'},$FORM{'alwaysaccept'})">
I am unsure if this API1 function has been ported over to have hooks support as described in /usr/local/cpanel/hooks/README