I'd close this issue as "won't fix" because as you said, it's a behavior of Commons Configuration (see https://commons.apache.org/proper/commons-configuration/javadocs/v1.10/apidocs/org/apache/commons/configuration/PropertiesConfiguration.html ).
Now we can achieve the need by escaping commas, as in:
myproperty=value\,with\,commas
See also https://stackoverflow.com/questions/6307318/apache-commons-configuration-loads-property-until-character