It's true that python is in a similar boat. This is part of the reason I custom-install python a lot on my boxes. It lets me ignore problems with the packaging of needed eggs, etc.
That being said, it's a real pain to maintain. And adding Ruby, with it's brain dead way of determining where things should go, just adds to the pain. (And yes, I know how to change all that, but it's a major pain in the neck. Things like that should be configurable on a system level, not with stupid ENV variables, without manually changing rbconfig.rb).
I totally agree with the criticisms raised in the article. We ship ruby in a commercial product and it's a total pain in the a**.