Resolution:
Please use the following workaround:

1. Create another attribute in Master Catalog e.g. CustomerID1 of type String.
2. Set the value of this attribute to some value say "NOTDEF" when the CustomerID is empty and "DEF" when it is not, through the validation rulebase.  Also make CustomerID1 attribute hidden so that end users don't see it.  I've attached the rulebase here for your review that can be used as a reference.
3. Create a condition xml which uses "equals" ProgrammingOperator for CustomerID1 attribute (see the condition xml attached).
4. Add this condition to your rule domain xml.
5. Create a rule template and select this condition.
6. Create a rule and provide a value "NOTDEF" for the "Customer ID1 is" condition.  This time you should be able to save the rule.
7. Now verify if you get the desired results.

When I use ProgrammingOperator isEmpty in the CONDITION (which checks for an empty value of attribute say CustomerID) for a Business Process Rule, the rule could not be saved.Is there any workaround?