At the moment I have a system (which I am going to recode, when/if I get back to coding the engine) where events are specified as just an array. I'm going to change it so that it's still an array, but elements in that array are "actions". For example, the room manager thing will have a "changeRoom" method that returned an action. The actions would then play out in order, with the next one occurring after the previous and all that. This should handle a lot of things like menus and stuff as well, with the ability to cancel.
So basically, the "scripts" will be a JS file, basically. Maps are also JS file, but really they are just a single function call with an object, so maybe in the future I could change it to JSON. I don't really intend to encrypt it though, since it probably isn't that hard to decrypt it.