In addition to GNU/Linux, Debian 6.0 will support GNU/kFreeBSD, which is GNU userspace (including glibc) on the FreeBSD 7 or 8 kernel.
From the point of view of applications, it's basically the same as Linux, so having ioquake3 treat it just like Linux seems like the way forward. (In particular, because kFreeBSD uses glibc and not BSD libc, it needs to include the same header files as Linux, not the same ones as FreeBSD.)
I don't run kFreeBSD myself, so I can't say whether this patch actually works, but the ability to compile is a good start...
Created attachment 2398 [details] patch from Cyril Brulebois