I think there is some flaw here on exactly how rennet is used to make cheese. Just because it is an ingredient directly sourced from an animal, or contributes its enzymes to process milk (I wouldn't say digest), does not make it any different than if you combined any other type of animal source probiotic (like high meat) with butter fat and labeled that a paleo food.
on Rennet:
Traditional methodDried and cleaned stomachs of young calves are sliced into small pieces and then put into saltwater or whey, together with some vinegar or wine to lower the pH of the solution. After some time (overnight or several days), the solution is filtered. The crude rennet that remains in the filtered solution can then be used to coagulate milk. About 1 gram of this solution can normally coagulate 2 to 4 litres of milk.
Today this method is used only by traditional cheese-makers in central Europe: Switzerland, Jura, France, Romania, and Alp-Sennereien in Austria.
Modern methodDeep-frozen stomachs are milled and put into an enzyme-extracting solution. The crude rennet extract is then activated by adding acid; the enzymes in the stomach are produced in an inactive form and are activated by the stomach acid. After neutralization of the acid, the rennet extract is filtered in several stages and concentrated until reaching a typical potency of about 1:15000; meaning 1 gram of extract would have the ability to coagulate 15000 grams (15 litres) of milk.
http://en.wikipedia.org/wiki/Rennet---
obviously even before actual cheese making, this is a less natural process than butter, which requires no additives or equipment.
Although, I agree with Alphagruis about the Africa comparison. I don't think one needs to argue dairy as a food ancestors a million years ago would eat, only whether it is compatible food, or supplies sufficient fats and minerals that may be difficult to get by some trying to mimic but not replicate what a paleolithic diet would consist of, in nutrition, not actual dietary contents. Whether it applies, and without side-effects is open to debate. But, merely saying it was non-existent practice, is not suitable proof, as cow and orange in that respect are as -or more- neolithic, as milk would have always existed in mamels, although likely not consumed by other species in any quantity.