Interestingly Ctrl W can actually be captured in Chrome now (on desktop) if the application is fullscreen and they make use of the keyboard lock API. I'm away from my desktop at the moment - can you try it on Chrome? (if you were using another browser). If it doesn't work we should file an issue and suggest they look into the keyboard lock API!

In our product (https://www.awingu.com/), an HTML5 RDP gateway, this actually works properly across browsers.

I had the same problem and just used a node-webkit shell to override the shortcut.

It works amazingly well. I use it to work on my EC2 spot instance and works very well even behind a strict corporate proxy.

If you need the shell, please ping me on my email.

Use an on-screen keyboard on the Remote side