I think you would either need to write a macro or use scripting to do this. If you're pretty computer savvy have a go with mortscript
http://www.sto-helit.de/modules/edito/content.php?id=38 and see if you can't make it do what you want.
Edit: Looking over MortScripts list of commands this definitely looks do-able. It's got a function to evaluate the current screen format (landscape or portrait) and another one to rotate 90, 180, or 270 degrees. So you can do an if then statement to check whether the screen is in portrait mode. If yes then rotate 90 (or 270) degrees) and launch Notes. If no then launch Notes. Then do a runwait for Notes to exit, and rotate 270 (or 90) degrees back to portrait.
Play around with it and see if it works.