They say in the book that house elf magic is different than human magic. That's why the house elfs can apparate in and out of Hogwarts. I don't think the Malfoys can block house elf magic from their house.
I’d bet they probably could, but it would be different than the normal anti-apparation charm. And of course the Malfoys being elitist pureblood jerks would probably never bother to sully themselves with magic geared to deal with house elves. Ego and the blind spots it creates is a recurring minor theme of the stories.
If wizards couldn't block elfs from aparating into/out of certain places, then anyone who had a house elf could go anywhere he pleased.
I think it works much better to say that wizards can, in general, block house elves but will often choose to make exceptions.