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I am not surprised that simply killing the processes doesn't work well. rqt doesn't know that the subprocess has been killed. The solution here would be to implement a --command-stop-plugin option. Since you can already perform this task through the UI it shouldn't be too difficult to expose it as in the CLI.

The problem you have with switching the perspective from the command line sounds like this ticket: https://github.com/ros-visualization/rqt/issues/108