Malte,
I'm not keen on changing my beloved location of files, but when you build the package for Debian I was wondering if there is need for adaptation.
There is not necessarily the need to adapt the OpenACS distribution/ file system per se. That's why there is packaging logic for Debian (dpkg-*) and all the other flavours that allows to separate these two concerns. From my experience, a formal packaging process always leads to clean-up in upstream.
However, I would definitely not align OpenACS to a single what-so-ever distribution of hosting platform, e.g. Debian file system layout or Debian Policy layouts.