Same problem here. Looks like Bean Loader.app (the GUI) and bean CLI cannot be installed on the same system. I did some poking around.
When you 'associate' from either the CLI or the GUI, files are installed into Arduino.app/ to do the interop with the Bean tools. No problem in theory. However the SDK and GUI use totally different techniques to interop with the Arduino compiler. The file that does the heavy lifting is:
When you associate via the CLI, this file is a python script (whose purpose is to drop compiled sketches into ~/beansketches for the CLI to find). When you associate via the GUI, this file is a compiled program - I have no idea how it works, but somehow it sends compiled sketches to the GUI.
The following file tells Arduino whether to execute the post_compile script directly or by calling "python filename":
So the symptom you are seeing is that Arduino is trying to pass a binary file to python. Oops!
The root cause is even more surprising - the GUI doesn't actually copy its files into Arduino.app, it symlinks them, so when you later run
bean install_bean_arduino_core, it actually modifies files in 'Bean Loader.app'. That's why simply reinstalling Arduino doesn't fix it. Try deleting both Arduino and Bean Loader.app.