Originally I come from a SysAdmin/DevOps background, so this is my favorite topic to talk about
I believe that deployment is hard with any stack - regardless whether you place a war file in an application server or copy files manually from A to B. As you said, it's important to have tools in place that ease the deployment while at the same time keeping security and integrity intact.
With Node.js applications you typically need some complicated build chain, usually involving npm, grunt, gulp, or some other Maven/Ant like build runner. Meteor comes with the
meteor command line tool that greatly simplifies this build process. Upon issuing
meteor build you get the equivalent of a war file that can be deployed. The path of least resistance in the Meteor-verse is to use
meteor-up or simply: mup. This will do all the heavy lifting for you, including setting up the proper Node.js and MongoDB instances and even performs the build.
That said, most developers go the mup router and have a single-command-deployment today. All you need is admin access (root or sudo) to a Linux or Solaris box. mup works with Ubuntu/Debian, but perhaps someone has forked it for the RedHat family already (I'm a fan of toy story, so I did most of my work on Debian, left Red Hat way before Meteor saw the light of day...).
In the future, the creators of Meteor plan to provide a hosting platform called Galaxy, which can be glimpsed on already by using the
meteor deploy command. This lets you host your app on the meteor.com infrastructure for free, but also without any guarantees or SLAs. Eventually Galaxy will be an easy place to host applications.