This question pertains to the nature-nurture debate, as can be seen from the topics given as examples (IQ, religiousness) even though the terms (innate vs. "social") aren't the usual ones.
There is an answer on this site about the debate regarding the heredity of IQ, but it does not address the question of the source of the strife that accompanies this debate.
In a recent seminar, we read Michael Rutter's book Genes and Behavior: Nature-nurture interplay explained, which I can recommend for an understandable and (rather) dispassionate review of the debate. He also focuses on IQ because it is one of the most contentious but also best-researched of such topics. He's not too flexible on ethics, so you might want to look to other authors for less retricted viewpoints on the ethical aspects. I think he does a great job pointing out methodological concerns and their implications.
Is it settled?
If by settled, you mean settled either way, I'd rather not reply, because usually you can always find some hypothetical counter-argument when you come up with something.
I think it's instructive, however, because it shows that the variation in nurture and nature matters.
For example PKU used to entail a dramatic reduction in IQ and it is definitely due to the genotype – however, now that the process is understood and the afflicted maintain a special diet, there is "nurture" variance – some people know about that diet and maintain it more or less well. Before that diet was known, the environmental variance was low. This would also affect the hereditity quotient of PKU.
If by settled, you mean do academics agree, I'd say, yes. Those who consider both biological as well as environmental factors (for example psychologists like Rutter, biologists, some sociologists like Udry) in their analyses usually find some agreement: environmental as well as biological factors and their interactions matter and you can also arrive at conclusions which factors explain how much variance (in, say, IQ). However, it is complicated and in the case of IQ for example, the degree of social variance (for example mandatory public school vs. only the privileged have any education) and biological variance (a small town, where everyone is related) play a role.
Of course there are contentious debates even among those academics who agree that both factors and their interaction play a role. For example, the Flynn effect (IQ test scores rose in the developed countries in the last 100 years) has been the matter of contentious debate (in short the hugeness of the rise isn't easily reconciled with the huge portion of variance explained by biological factors), but I think few who are actually involved in that debate would say "maybe we'll know in 1000 years". Instead they peddle their pet theories from heterosis to prenatal environmental influence etc., but that's just science in progress.
In the answer you linked to, I suspect appealing to lack of clarity was an attempt to stir some dust up, so as not to concede being wrong.
I think the contentiousness of these questions stems from the fact that to the uninformed some of the conclusions seemingly conflict with dearly-held convictions like equality of chances. I think truth should not be judged by what "ought to be", but for any individual it's hard to keep them apart in every line of thought. But among serious academics these convictions probably only make some round their estimates of heredity down or up, not reject one source of variance out of hand (well you can probably find someone who still does, but I doubt they could answer a few simple questions about their premises correctly).
