As per the link, Mule Anypoint Studio application launcher now supports launching multiple applications and it works. I could not find how to stop individual application if multiple are deployed?
You can't. Studio's console refers to the JVM instance running the attached Mule distribution, not to each individual deployed app on that instance. However, if you modify any app config file, that app will be redeployed.
On the other hand, reviewing the log you can see that each app is deployed independently from <workspace>/.mule/apps/<app-name>.zip. After its deployment, a file named <workspace>/.mule/apps/<app-name>-anchor.txt will be created, if you remove that file the app will be undeployed.
HTH, Marcos.