Should the JmsTemplate bean be declared as a prototype bean or as a singleton? I think either option is reasonable and it seems to me it's mainly a question of how Spring implemented that bean but I keep finding conflicting reports about the use over the net.
JMSTemplate like most of the spring templates is thread safe after creation so you should leave it at scope singleton.
If the runnable is implemented as a inner class it can access the instance variables of the class in which you define it. This can be a spring bean with all the required dependencies (jmsTemplate etc) injected into it.