Earlier quoted context omitted.
Did babel force you to upgrade right when version 6 came out? They bumped the major version, that should be a pretty clear indicator that existing workflows will break. Whenever you use a tool, you're accepting risk for the reward you're getting from it. If I run Gentoo on my servers, it's not really fair to complain when an update breaks something.
JavaScript world is known by moving fast and breaking things (which is fine for me, I learned to respect this culture). So, when a new version of some popular framework or tool comes out, there's a very real risk that the previous version will be abandoned really soon and left without support from developers and community (I was burned by it quite a few times). So no, had to move forward like everyone else.
Your whole situation and outlook really seems to be blaming anything but yourself for mistakes that you made.