why not using state activity instead? I think it is perfect to put application A process in wait after signaling application B. Once application B is done with its work it will signal back application A to continue with the flow.
About JMS, jBPM 4.4 has support for JMS integration but only outbound traffic, so you shall use another technique to trigger process to continue... For more information about JMS activity take a look at dev guide http://docs.jboss.com/jbpm/v4/devguide/html_single/#jms