How to set -Dorg.apache.el.parser.COERCE_TO_ZERO=false programmatically

You can set the system properties programmatically using System#setProperty().

System.setProperty("org.apache.el.parser.COERCE_TO_ZERO", "false");

However, you need to ensure that this is been set before JSF/EL ever get initialized. Best place would be a ServletContextListener.

public class Config implements ServletContextListener {

    @Override
    public void contextInitialized(ServletContextEvent event) {
        System.setProperty("org.apache.el.parser.COERCE_TO_ZERO", "false");
    }

    @Override
    public void contextDestroyed(ServletContextEvent event) {
        // NOOP
    }

}

Register it as <listener> in web.xml, or when you're already on Servlet 3.0 (Tomcat 7 and so), with @WebListener annotation.