I've taken the resources referenced in this issue and have combined them into one package: http://github.com/jimbrowne/apache-crowd-cookie. I found patching the on-disk version of Atlassian's libraries to be a distraction, so I renamed the module to CrowdCookieAuth and made it self-contained. I also added functionality to the sample login.cgi to handle logging out as well as redirection after login in addition to pulling code into the CGI to avoid patching Atlassian's libraries.
I hope that the status change to "short term roadmap" means Atlassian will incorporate these changes or otherwise directly support cookie-based authentication in Apache.
My preferred solution is a binary Apache module and if I have the time in the future I'll modify mod_auth_openid to support Crowd as I prefer the all-in-one approach (i.e. no need for a login.cgi)
Working on it