I have to host a JRuby on Rails application on Mongrel. However , I have to support mutual authentication. I understand which i could just host it behind a Apache with mod_proxy use mod_ssl to pass through the cred or area of the cred like a request header to rails. However I want the entire stack to become Java. It is possible to Java application server that may do mod_proxy + ssl type of configuration without me needing to install Apache. Also, we want this to become platform independent. IIS or Apache+OpenSSL is really not really a preferred alternative.

What other deployment designs will also be welcome.

I'd really recommend using either jetty or glassfish for implementing your application. You are able to run mongrel in JRuby, but it is very slow and no more positively maintained. I certainly wouldn't apply it a production enviroment (in JRuby a minimum of). I've found jetty to become more lightweight, both suppport SSL (Jetty, Glassfish).