In Visual Studio (VS 2015 in my case but it’s similar down to VS 2010 at least) keyboard shortcuts may have a different meaning depending on the context in which they are executed.
Click Tools / Options / Environment / Keyboard to look up or define shortcuts (you already did that probably). What I called “context” is selected in the combobox labelled “Use new shortcut in:”. Most likely you defined the shortcut in “Global” but you want it to work in “Text Editor”. In the latter Ctrl+W selects the current word.
Redefine Ctrl+W for “Text Editor” and you should be fine.