I actually think it didn't hurt the web, it was a massive driver for change, Flash highlighted the lack of functionality in html/js and was part of the reason that forced html to finally get canvas, etc.
If you're completely honest with yourself, you'll realise that html/js are still years behind what you can do in Silverlight and Adobe Air.
Now it's mobile apps that are forcing the web to carry on evolving and highlight just how backward html/js is. In years time we'll have people saying that phone specific apps were terrible, but in reality, without something to show us the flaws of html/js are, it wouldn't move forward.
Personally I'm no fan of the mono-culture of the web, the idea that you can only use one language, either for markup or for programming, should be anathema to all of us and instead it is bizarrely celebrated. I'd far prefer to be using Python or Ruby or whatever than javascript and in reality I think it's probably costing the world billions or trillions in wasted effort as we schlep around with javascript.