I've written a simple shell script as a replacement for gs (since I constantly forget if I was in a sub-shell or not). All it does is change $GEM_PATH and $GEM_HOME when $PWD changes (while staying in the same shell). If the current $PWD has a directory ".gs", `gem install` will install them there instead of globally. All I have to remember is to create a .gs directory when I start a new project.
It does not address all issues highlighted in the article, nor do I know how well this would work in a production environment with automated deployments. It's probably more of a work around than a solution. I vastly prefer it for personal projects, though. Hate solving gem conflicts with "bundle exec".
[1]: https://github.com/soveran/gs [2]: https://github.com/cyx/dep