This API will allow you to choose which streams get transcoded:
How to control which streams get transcoded using server-side API
You can also match template names with stream names, and remove the specific template name (i.e.transrate.xml, transcode.xml) from Application.xml file.
if you only have a template named myStream.xml you will only transcode streams named myStream. if you also have a template named yourStream.xml, streams named "myStream" and "yourStream" will be transcoded using those templates, and other streams will not be transcoded.