How did they break it? If you don't install ruby from apt, you won't get the debian version of ruby or rubygems, and nothing is broken.
Is it reasonable to expect the apt version of ruby + rubygems to play nicely with an arbitrary compiled version that is installed in PATH? It would be nice, but few packages work this way.
It's reasonable to expect that apt's Ruby/Rubygems works with Bundler in the same sense as it's reasonable to expect that apt's Apache will set the right MIME type for a ".html" file, and not set it "application/binary" by default because some configuration file some Debian person thinks should exist isn't there.
Put more simply: if they can't package a rubygems that actually works with the rubygems ecosystem, they should not package rubygems at all.
After their changes, the tool does not function as it was originally intended. Certain sections of the official rubygems documentation give instructions that do not work with the Debian version of rubygems. How is that not broken? In what way did they not break it?
I understand and admire Debian's commitment to cleanly built, working software. Within that context I also understand that rubygems is a big, scary unknown. That said, if the only way to solve the problem is to hack up rubygems until it no longer works as intended, the only real answer is to not ship rubygems within Debian. It just flat out has to be left in "here be dragons" land. As things are right now people just get pissed off that Ruby isn't working correctly under Debian, then they have to go play with dragons anyways.
Is it reasonable to expect the apt version of ruby + rubygems to play nicely with an arbitrary compiled version that is installed in PATH? It would be nice, but few packages work this way.