Just add the following to your Intercom initializer which was generated by the intercom-rails gem. It disabled the messages module completely, so you can implement your own version using the API directly.

intercom.rb

# Add a disabled modules configuration to the script tag configuration
module IntercomRails
  class ScriptTag
    alias_method :original_intercom_settings, :intercom_settings

    def intercom_settings
      hsh = original_intercom_settings
      hsh[:disable_modules] = ['messages']
      hsh
    end
  end
end