Sorry, it's late for that ... (it was part of the import process).
Would it be possible to make the automatic conversion (A) to (B) when Kune.cc receives such URL request? That is, Kune already checks the hyperlinks searching for patterns, to know if the link is local or not. Now it would be another pattern (kune.cc/#googlewave.com) that would be modified (kune.cc/#kune.cc).
PŜ: If it's feasible, I could do it myself.