I'm not sure if this solution has been suggested, but I just noticed that the gmail threading algorithm ignores the bracketed part of the subject line. (I couldn't find it documented officially, though).
That means that if JIRA subject lines can indeed be customized to say e.g. "[JIRA - Created:] (LUCENE-XXX) blah" instead of the current "[JIRA] Created: (LUCENE-XXX) blah", the gmail issue would be resolved. I only noticed it because this is exactly how YouTrack handles this. Is this a viable option?