Follett, you can also get it to work by writing a javascript plugin as mentioned before. It's just external javascript can't reliably call in to the Construct 2 engine. There are various reasons for this: the minifier and obfuscator, the complexity of the engine, and so on. Writing a plugin is probably the easiest way, or AJAX if you're making requests to other pages.
I find this tool pretty useful: javascript obfuscator javascript-obfuscator.org