It's kludge plain and simple. It's ugly but it works (well kind of). That's the exact definition of a kludge. Further interesting things with wp-cron is that since other plugins make use of it, if you do have a "real" cron implementation the advice is to use the real cron to trigger wp-cron (via curl hitting a localhost only accessible page). Again, it's a kludge but it keeps things running.

On the topic of new stacks from the OS on up, Docker[1] (and lxc in general) and CoreOS[2] are really cool. It's a much more elegant and long term solution to packaged, yet controlled, environments.

[1]: http://www.docker.io/

[2]: http://coreos.com/