Hi there. I'm a Linux System Architect, which means I work from the CLI a lot and have more than a passing knowledge of security. I frequently have a need to add notes out of a terminal, and copy/paste is not my favorite activity. I'm not pleased about the lack of CLI tools in Evernote. I run OSX and don't particularly feel like figuring out how to write Applescript to accomplish CLI note access.
After reading this thread, I fail to see how Geeknote is doing anything that any other client or integration could be doing or, for that matter, a sufficiently coded TamperMonkey script or something. It seems to me like there are far more effective methods that could be used to slow or block unauthorized access to accounts that would not punish legitimate customers that want to use geeknote. Perhaps you could just generate oAuth tokens like you do with developer API tokens, and include a security disclaimer about storing said tokens? Alternately, adding CLI tools to the Evernote for Mac client would scratch my particular itch, but clearly there are lots of linux users that want access to their notes from the CLI too.