I think JavaScript embedded in websites is one of the most important abilities in the web today. It's critical to the way nearly all modern applications are written and it allows for extremely fast and rapid development of scalable powerful applications.
Awesome, no?
If my site would best be served by Lisp, or Haskell, or Java, or Javascript, or C#, or Python... let me decide. It just feels like we've entered this world that everything has to be Javascript, if its appropriate or not.
For example, the fact that you say there'd be plugin-hell with 30 plugins is crazy. A good management system should be able to efficiently handle hundreds or even millions of components.
And what if we standardized support for the scripting languages? So, for example, the DOM calls looked like RESTFUL services returning JSON. And maybe there was a low-level, but efficient virtual machine that everyone could target (someone mentioned LLVM -- although I really don't care what it is all that much).
It just feels like the web is in this weird cycle where we continue to make suboptimal choices... largely because that's how it was done the first time.
The thought that developers should wait for browsers to catch up with their needs is what leads to such situation. But, if the JVM finally decided to host other languages, after they got a lot of attention, maybe so will browsers. But we need to justify it first. Not wait.
Anyway, malwares would have spread through downloaded executables (e-mail attachments, etc). Is Javascript even helpful to most malwares?
Yes, very much so. Adobe PDF reader's JavaScript ability is the reason it's dangerous to open PDF files anymore. They issue a new patch once a month it seems and are working on a sandbox as the problem cannot be contained. Without JavaScript embedded in the PDF files, this would be a much more manageable issue.