The error which you have posted in your original question is related to configuration. Refer this article for further help:
http://wiki.scn.sap.com/wiki/display/EEM/Troubleshooting+7.1
Now, coming back to your original problem, if I am not wrong, you want the process instances running on the erroneous version to stop executing until the correct version is deployed (Please correct me if I am wrong).
Since you have mentioned that the infinite loop is present in an Automated Activity, there must be some EJB Method/RFC call in this Automated Activity. This means that your process server is going to communicate with this external entity to execute this EJB/RFC.
Suggestion:
If you see my previous post, in the image I have highlighted 'Deactivate All'. Just next to this button, is a link called 'Application Communication'(Application communication is nothing but a section where you specify the Provider Sytem to access the external entities like EJB/RFC).
Click on this link. It will redirect you to the Application Communication:Configuration section. Here, you will see theservice group/s of your BPM which access the RFC/EJB.
Select the Service Group and click on the 'Edit' button above.
Now, in the 'Provider Sytem' dropdown next to the Service group, select "None" and then click on "Save".
What this will do is, it will explicitly cut down the communication between the BPM and the EJB/RFC forcefully. So, when the process execution reaches the automated activity, the process will fail beacuse there is no commuincation provider for the BPM service group.
This should solve the problem at hand.
Note:
If the infinite loop is in the RFC/EJB, you can simply correct the code and deploy the EAR(in case of EJB) and then reset the application communication back to the original provider system. In case or RFC, suggest you to correct it and re-import in your BPM and reset the application communication back to the original provider system.
Regards,
Sid