Quick reply (thanks for the well-formatted cited text!).
* Java didn't have the bad security rep until relatively recently. Java had nice-looking UX in the 90s (Netscape bought Netcode on this basis), much nicer than Web content. Didn't help.
* Web != Desktop. Large desktop apps are the wrong paradigm on the web. You won't see a Web-based Mathematica rewritten by hand in HTML/JS/etc. You will see Emscripten-compiled 3DS Max (see my blog on OTOY for more). The reasons behind these outcomes should be clear. They have little to do with JS lacking Java's big-OO features.
* Large mutable-state collection libraries are an anti-pattern. Functional structures, when hashes and arrays do not suffice (and even there), are the future, for scaling and parallel hardware wins.
* Conway's Law still applies. Too often, bloated OO code is an artifact of the organization(s) that produced it. This applies even to open source (Mozilla's Gecko C++ code; we fight it all the time, including via JS). It definitely applies to Google (e.g., gmail, Dart at launch). Perhaps there's no other way to create such code, and we need such programs as constituted. I question both assumptions.
* Glad you brought up refactoring. It is doable in JS IDEs with modern, aggressive static analysis. See not only TypeScript but also Marijn Haverbeke's Tern and work by Ben Livshits, et al., at MSR. But automated refactoring is not as much in demand among Web developers I know, who do it by hand and who in general avoid the big-OO "Kingdom of Nouns" approach that motivates auto-refactoring.
In sum, if the web ever becomes big-OO as Java and .NET fans might like, I fear it will die the same death those platforms have on the client side. Another example: AS3 in Flash, also moribund. These systems (even ignoring single-vendor conflicts) were too static.
The Web is not the desktop. Client JS-based code can be fatter or thinner as needed, but it is not as constrained as in static languages and their runtimes. Distribution, mobility, full-stack/end-to-end (Node.js) options, offline operation, multi-party and after-the-fact add-on and mash-up architectures, social and commercial benefits of the Web (not just of the Internet) -- all these change the game from the old desktop paradigm.
JS has co-evolved with the Web, while the big-OO systems have not. This might still end up in a bad place, but so far I don't see it. JS can be evolved far more easily than it can be replaced.
/be