I'm curious as to what kind of problems you've had with deploying on the same server as Java applications?
As far as Rails deployment goes, yes, it's been a bit of a pain compared to PHP applications and the
J2EE world. Having said that, you do have tools like Capistrano which work wonders provided that you put in the effort of getting into the ropes. Once you're past the learning curve, it's devastating to go back to Java-land and realize there's nothing similar available.
Furthermore, if you've bumped into trouble trying to manage stray FastCGI/Mongrel processes, it might make sense to give Passenger (mod_rails) a try. Based on my short experience (two weeks), it's working quite well and is far more manageable than my previous FastCGI setup. And its performance seems comparable or even better than a Mongrel cluster.