well, since putting acls on scripts is ugly, and it allows root to start or stop services, what I do is put ACLs only on the stuff the init scripts start, and enable the ACL system after all the other init scripts are done.
Do you mean, you are setting the ACL for, let's say Apache, by setting the ACL on /usr/sbin/httpd rather than /etc/rc.d/init.d/httpd? Then you enabled the ACL system after all the init scripts has been run?
But what about if I want to restart the services at will?