Haha, this is a common question! I believe this is either before or right when some of the current team got involved with the project. TL;DR is probably just that Babel was compiling more than 6to5: 7to5, 8to5, ES2015toES5, etc. Babel is well known name regarding languages/translation via the Towel of Babel and Babelfish.
It's also our most commented on issue yet: (217 comments). In the end, Sebastian chose to go with Babel. James wrote a blog post on the rename: http://babeljs.io/blog/2015/02/15/not-born-to-die.