Another possibility might be just colloring variables and assignments (since thats where the scoping actually matters)

I was just thinking the same; when all my syntax highlighting in a region looks backwards, I normally assume I've got a mismatched quote just before it. I think I'd be thinking that with this all the time.

Subtle changes in the background colour would be a nice alternative.

It is a good idea indeed. I believe Notepad++ does background scope highlighting already, just not accurate enough for JavaScript specifically.

Exactly my thoughts, this could work really well if implemented properly.

Yes; highlight BG lighter grey. This would be an awesome plugin for ST.