As DoubleAA has already implied in the comments to this question, the overall principle that we should use to keep questions like the one linked above from degenerating into holy wars or the like is the same principle that we use in general to keep Mi Yodeya from being a host to holy wars: Keep all material on the site appropriately focused.
Keep question posts focused on specific, answerable questions about Judaism.
Keep answer posts focused on addressing the question at hand.
Keep comments focused on actionable suggestions for improvement of question and answer posts.
In the case of topics that may tend to excite immature or combative responses, it does make sense to be a bit more zealous than usual about enforcing these principles. So, if you see content that is not focused appropriately and that seems like it could spark a fight or offend readers, use the powers you have available to address that: edit, flag, comment, and vote (not necessarily in that order). If a particular post attracts inappropriate responses and seems likely to attract more, those with the power to protect the post may end up doing so.
In my opinion, the linked question and all of the comments on it at present (There are no answers yet.) are all appropriately focused.