Yes, this should be fixed upstream; a new DynamicClassLoader should only be set as the thread-context classloader if one is not already in place.
My first impulse upon seeing this was that this was "last straw" territory w.r.t. using clojure.main/repl (as recorded in the thread linked above), but the work necessary to stop depending upon it would be considerable (not because repl does much, but because interruptible-eval/evaluate is structured to cater to it). Some years on, and it's clear that this fundamentally a minor problem (insofar as hardly anyone has complained AFAIK), so a fix that requires e.g. Clojure 1.7.0 would be fine.