I have managed to solve the problem. Sharing here in case someone else finds
it useful

We cannot get Ctrl-W to vim, as it will be stopped by browser.

Send something else not caught by browser. For this purpose, I used Ctrl-j. 

On vim, I used commands like
:map <C-j> <C-w>w
:map <C-k> <C-w>gf

each mapping provides me an alternative way of getting the same thing done.
Now my ~/.vimrc is having these mappings and I don't have to worry about
setting these mappings anymore

In addition I made a new chrome profile just for going to Guacamole, and in
that profile I use AutoControl to capture and ignore Ctrl-W, so that even if
I type it by mistake there is no problem





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