Writing javascript takes a text editor and a browser.
Provided our modding api and game can be run in a browser, yes but it will hardly be the case with Terasology. And you can write Java in a plain text editor as good as JavaScript. (You have to comply to the interface-checker, be it a JS parser or a java compiler)
By the way: Nice story on your link.
I know of the differences between Java and JavaScript very well (duckTyping, Closures, etc.) and highly estimate them when programming JavaScript, but why the hell would you want to use them in a Java project? To use these features in Terasology we would have to map every of these JS-peculiarities to a Java-peculiarity which can be very difficult, not to say impossible.
managing a dependency chain, worrying about packaging, more dependency issues at deployment, etc
Dependencies are not here to bug you, but to help you building things out of existing parts (You have the same thing in JS when using jQuery etc.). By the way: That would in no way affect modding, as you most likely not depend on whole new libraries in your mods, so that's no point for JS.
For Modders...
... doing the same thing than in JavaScript, Java is in no way more complicated (assuming you're able to write "public void doSomething()" instead of "doSomething = function()") for a user/modder. Ok, you have to encapsulate functions into a MainClass but if you don't wanna turn your JS-Code (if it's more than a thousand lines) into chaos you make the same thing using classlike-functions, prototypes or simply files.
(If it makes sense we still could write the class-body around the code at loading-time, so you won't even see it while modding)
Of course Terasology code is more complicated than the average website's javascript code but it incorporates waaay more functionality than the average website.
So I still conclude that if we're designing the modding interfaces simple enough, there wouldn't be any significant disadvantage when using Java over JavaScript for average joe modder. (Even advantages because he can use IDEs with syntax-completion if he wants)
BUT for core developers...
... it takes a hell lot more to lay a Terasology-feature open for modding when using JS than using Java. In Java you only have to write a simple interface for your moddable coreClass, for JS support you would have to write a whole new syntax-checker and parser for every new moddable interface.
We could make a markerInterface "Moddable" which says the mod-classloader that this interface can be modded. This way it can limit the moddable-classes and eventually automatically export all modding-interfaces (using reflection) so that a modder only needs to download these for his modding job and not the whole Terasology source.
Any questions left?, Anyone else wanna try to convince me of another modding-language than Java? *MeLovesDiscussingSoftwareArchitecture*
P.S. One little drawback with Java for me as a developer I must commit, is the missing delegate (function=object) concept but I think a normal modder wouldn't fully understand them (with all side effects) anyway and therefore will not miss them if not present.