system.activationScripts.ldso = lib.stringAfter [ "usrbinenv" ] ''
mkdir -m 0755 -p /lib64
ln -sfn ${pkgs.glibc.out}/lib64/ld-linux-x86-64.so.2 /lib64/ld-linux-x86-64.so.2.tmp
mv -f /lib64/ld-linux-x86-64.so.2.tmp /lib64/ld-linux-x86-64.so.2 # atomically replace
'';
does the trick, making /lib64/ld-linux-x86-64.so.2
the third FHS exception after /bin/sh
and /usr/bin/env
Currently I see no better solution