OK. It's definitely the libsvrcore0 library. I just recompiled it myself with debug enabled (configure --enable-debug --with-systemd), copied it over /usr/lib/x86_64-linux-gnu/libsvrcore.so.0.0.0 and the directory server initialized the SSL fine and runs on port 636. The result is the FreeIPA upgrade finished fine. I guess it's not the debug enabled but some other compilation option - I'm not sure but it looks to me the default debian build doesn't use --with-systemd option?
-- Michal Kašpar