OpenJK doesn't start any new tasks, the TLSF_FreePooled warnings come from whatever happens to run at the time. In OpenJK all the memory is allocated either via malloc/calloc or C++ new (the two are not mixed), so this shouldn't be a problem anyway.
Things start to go south after the game module (jagameppc.so) is unloaded. Is it safe to use dynload.library with C++ code? I use the LibNIX initialization from RTCW, with some comments from the SDK's nixskeleton.