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.
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|# Add a disabled modules configuration to the script tag configuration|
|alias_method :original_intercom_settings, :intercom_settings|
|hsh = original_intercom_settings|
|hsh[:disable_modules] = ['messages']|