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
You might also take a look at the Microsoft.BizTalk.ExplorerOM.dll. It is contains business level objects that are pretty nice to interact with in .NET code. You can find the dll in the installation directory, mine is at: C:\Program Files (x86)\Microsoft BizTalk Server 2009\Developer Tools
Here is the MSDN documentation on it: http://msdn.microsoft.com/en-us/library/microsoft.biztalk.explorerom(BTS.20).aspx
And a good high level walk through of its use: Link