Supondo que a largura da tela (opção -W) seja uniforme, tente o seguinte
diff --expand-tabs -W 100 -y hpc.sorted.new.list bduc.sorted.new.list |
awk -v W=100 '(substr($0,W/2,1)=="|")
{left=substr($0,1,(W/2)-1);print left "<";
right=substr($0,(W/2)+1);printf "%" ((W/2)-1) "s>%s\n"," ", right;
next;}1'