Hello Ivan,
Breaking existing (possibly automated) systems is a _very good reason_ IMHO :). Sure, warn the operators that they're using a legacy system, deprecate the option but don't disable it.
https://trac.torproject.org/projects/tor/ticket/18054 sounds like a pretty sane solution btw.
Even if it's no longer officially supported, I think OnionCat in its current incarnation is a great proof of what could be done with the Tor network, other than privacy protection. I actually have this listed on one of my slides for SIM4Things - it's good for the Tor network, shows it can be used for a variety of things while putting very little stress on the network components. Very little traffic, potentially large PR impact (in a good way :) ).
Razvan