I can tell you that beef allergies are not unheard of. Here is a brief discussion of it, from which you can see that it is a relatively rare thing. But note that beef allergy is more common among those who have cow's milk allergies, which seems to make sense (see here).
This has made it into the paleosphere most prominently recently in two posts on the topic by Matt Metzgar (here and here), which have been noticed by Masterjohn and Jaminet already. In the second post Metzgar finds the study he was looking for (abstract), which claims that among Argentines with pre-existing skin conditions, asthma, or digestive conditions, 57% were allergic to beef. Brief extract:
After the exclusion period, subjects
with skin and stomach problems were
able to tolerate beef again. Subjects
with asthma still were not able to.
The authors believe that intestinal
permeability was the factor that made
beef allergenic.
So what's going on here? You would
think beef should be normally
tolerated. First, results are
different country to country. For
example, in Chinese subjects with
eczema, there is a low prevalence of
beef allergy. Yet in this same study
it says:
"Specific IgE levels for beef
correlated with all the other
food-specific IgE levels."
Here's my educated guess: once
intestinal permeability is created via
other allergenic foods (wheat, milk,
soy, etc.), then beef proteins become
allergenic.
This seems to be right in line with what you proposed. Some other digestive damage has been done, which allows things to sneak into our system that usually can't. When the other damage is fixed, beef again becomes easily tolerated.
The other thing I would propose--although I haven't looked at the full study--is that there's something else nasty that gets onto the beef in Argentina during processing that people are allergic to. I don't know much about what happens to beef in Argentina (I have heard it's very tasty at least) but I'm sure you can imagine that being an issue here.
I would conclude though that intolerances and allergies are very individual things: some people even have a lot of trouble with sweet potatoes, for example. We shouldn't let the mere presence of allergies to staple foods distract us from the fact that they generally are infrequent. In most cases it was something else that did the damage first: wheat, soy, etc. But even when it wasn't, the point still holds. People will occasionally be allergic to things, that's just life.