I don't think there's a way to omit workspace files from the Ctrl+O search.
Maybe you could re-map your workspace to only include files that are relevant to your site.
For example, say you mapped ~/company_dir, which includes your site and a bunch of other projects from different teams. Your site is located at ~/company_dir/a/b/c/d. You could just map this more specific-directory, instead.
That last suggestion probably won't help, but it's worth a try