On my machines, I don't allow an Estop reset until the control is up and running. This prevents any startup weirdness, but uses an output. To do this just put one of the outs in the Estop circuit and turn it on in startup.fil. Also, turn it off in shutdown.fil
It sounds like you're trying to get by without an IO card. You may try asking Galil. They have a great forum on their website.