How may I prevent CTRL+R in the program editing window moving the focus to the output window each time?
(This does completely describe the problem.)
If you're talking about the shortcut of ctrl+R running your sketch from the Processing editor, then there isn't a setting to disable that.
However, Processing is open-source, including the Processing editor. So you're more than welcome to download the source, remove the shortcut yourself, and run that instead.
Similarly, if you want to shift focus of the window back to the editor, there isn't a way to do that from the settings. But you could modify the source to make that happen pretty easily.