The Ruby/Rails way: When the drama created by oversized egos inevitably comes to a head, fork/replace the project and badmouth the other guys.
Allow me to rewrite your statement to be ruby-drama-free:
We have been working on several JavaScript-related tools that build on top of RubyGems. As the most recent versions of RubyGems have begun deprecating standard APIs that we and many other projects rely on, we have decided to fork the project, with the intention of maintaining an alternative to RubyGems that maintains ongoing compatibility with the existing API.
<optional: insert rational for forking / discussion of how you would prefer to merge and not use the nuclear option of forking someone's project here>
People love to create meta-drama about the ruby drama, but really, let's not sugar-coat it. These are significant and serious breaking changes to the standard package manager, in a point release. Something is wrong.
Allow me to rewrite your statement to be ruby-drama-free:
We have been working on several JavaScript-related tools that build on top of RubyGems. As the most recent versions of RubyGems have begun deprecating standard APIs that we and many other projects rely on, we have decided to fork the project, with the intention of maintaining an alternative to RubyGems that maintains ongoing compatibility with the existing API.
<optional: insert rational for forking / discussion of how you would prefer to merge and not use the nuclear option of forking someone's project here>