Python Pip vs Ruby Gems
I think you should raise your problem about gem/debian and what are you going to do with it specially.
I am using pip and debian now and still no problem by now.
I mostly do work in Python, but I have been using some of the Ruby stuff for Server Configuration Management (ie Puppet and Chef).  I also use Ubuntu/Debian as my primary Linux distro for servers.
Why is there a weird Debian/Ruby conflict over Gems, and not a similar showdown between Debian/Python over Pip?
Personally, I don't mind installing newer packages then the "system" approves of.  I know Debian wants to make a stable system, but when I am running my own application code on the server, I can guarantee you it's not stable to begin with.  
Anyway, I would be interested to know if Pip is doing something different, or if it's an ego thing or whatever?