Are they actually complaining that using a transpiler needs configuration? Also if-it-ain't-broke-don't-upgrade-it? If they liked Babel v5 why jump on v6?
But yeah in node land if you don't upgrade to the latest major you're going to be left behind in bug and security fixes (good luck finding projects with actually maintained LTS branches and if they exist they're almost always the previous major version and nothing further back).
(Got myself burned with Babel6, too)
If you write your web back-end in C/SQL its likely that it will run unchanged for the next couple decades.
If you write your web back-end in PHP, it will probably run with only minor changes for the next 5-10 years.
If you write your web back-end in node.js, you will be lucky if it runs without modification in 6 months.
Just because something is cool, or easy and fast to bootstrap doesn't make it the best choice for a long term successful project. Its like people used to say about delphi vs visual basic, "Delphi makes the easy stuff easier, and the hard stuff doable. Visual basic does the easy stuff for you, but makes the hard stuff impossible." I think that applies to a huge number of recent "technologies". Careful use of make, RPM/deb and kickstart will solve all the same problems as $COOL_NEW_TECHNOLOGY. It might take a little longer up front, but 5 years down the line when your project is a million lines of code across multiple platforms and languages with differing dependency tree's/etc you will be thankful you didn't tie yourself to a build environment designed for a particular language/enviroment. Especially, if said technology gets abandoned and you end up maintaining it in-house.