I've got a solution which I setup / cleanup using batch files ... - there are a pair of MSMQ ports, send and receive, with another application on the end of the queues
I'm finding I can't properly stop the orchestration in the batch file ... the error is the send port is unenlisted - I'm using the StopOrch.vbs script from the SDK samples
But I can go into BizTalk Admin Console and manually stop the orchestration with Full Terminate Ok
The setup / cleanup works Ok if I don't actually push any messages down the MSMQ queues