But you need to write your frontend SPA with JS. And the isomorphic part, if designed from the ground up adds almost no extra code. So, really it's almost free to render first with Node, if you're starting a fresh SPA. I don't see why you wouldn't want to do it.
And we can all agree the ES5 has some warts, so you may as well transpile. Whether it's ClojureScript, Coffee, Type, or anything else doesn't matter, I just think it's a problem solved. Webpack makes debugging them easy with sourcemaps and live-compilation. In fact you can get hot-reloading[1] in React. So your app re-compiles without reloading.
I'm happy with ES6 + Flow. It's all ES6 syntax anyway, works with all libraries, and is fast to write, good looking, and functional.
Given JS has first-class functions, and many libraries to follow functional patterns. You can write very stable code, with almost no chance of side effects within a given function/context.
I did, on the other hand, have to take over cobbled together jQuery, Backbone and Coffeescript applications.
Yahoo is writing a greenfield application, and they are avoiding exactly those problems by using React. So, literally your pain point is exactly what they are writing about avoiding, and yet you still comment on this article with the same anti-JS nonsense.
For frontend development, a lot of frameworks and libraries only work consistently with Javascript. I've looked at TypeScript for instance, and it indeed looks nice. But it has a bunch of edge cases with Angular and/or Backbone. You're just piling on complexity with these languages.