The Gemara says that R. Bania was measuring the area around mearat hamchpela to mark off the area. Presumably this would be to notify kohanim where they may walk and where to stay away from and anyone else who wished to remain b'tahara and free of tumas mais.
Firstly, the present structure around mearat hamchpela is said to be Herodian. If it was built by Hurdus it would have preceded R. Banai by quite some time, perhaps a few centuries. If so, there would be no need to mark off the graves of the Avot, Imahot, and Adam and Chava. The whole building is an ohel.
Secondly - doesn't it say somewhere that the bodies of tzaddikim are not metamei? It seems that this memra is not actually how we posken the halacha though.
Dear Mr. Kosofosky
Hello there and thank you for your interesting question. The truth is that this question is already brought as proof by some Poskim that the tombs of Tzaddikim are Metamei (see Yechaveh Da'as, Vol IV page 290).
I will, however, make a suggestion based on archeology. The structure is indeed Herodian preceding Rebbi Bena'ah as you pointed out. However, the Herodian structure consisted of a floor and four walls. There was no roof at the time. Thus if there was no Pose'ach Tefach from the bodies till the roof of the cave, the Tumah rises through the ceiling of the cave and is Metamei those above the floor.
People who have descended into the cave in recent years have discovered that many bones were brought later on and placed into the cave. Thus it is possible that the Tum'ah issue we're dealing with here is not that of the Avos, but rather of the bones that were placed in the cave. This would explain why Rebbi Bena'ah had to measure the extent of the cave, as opposed to marking the location of the Avos.
All the best.