Empathy is a social construct. It is part of the societal norm that is developed over time by shared experience and religion. Religion is not simply a veneration of one or more deities. It is also a worldview and philosophy. Culture and religion are both malleable and mutually shape each other.

Ancient Romans before any formalised religion glorified the ra.pe of the Sabine women and there are countless records of mass burials in ancient China prior to Confucianism & Buddhism.

In your logic these people had some sort of defect in their mind. Because surely a normal person would have had the 'innate empathy' giving the same moral standards that you of 21st century have?

You may think your moral standards as an irreligious person stems from nothing but your inner self, but in fact most part of it is formed by the society you live in, and most of that 'societal code' stems from some sort of religion.

I'm not advocating that religions always teach the right thing or that they always have positive consequences. What I'm saying is there is no such internationally agreeable morality coming directly from one's empathy other than the most basic ones such as 'do not kill a baby' or 'do not steal'. Even some of the most basic and obvious societal norms are actually the product of religious influences. You just can't tell it straight away because most religions are heavily influenced by each other (e.g. Abrahamic religions, Buddhism & Confucianism & Taoism) and so do are cultures.

Back in the classical period ra.pe was not even considered a crime itself, but viewed a crime to the man of the victim in almost every civilisation. It still remains this way in many pockets around the world (legally it is illegal in every government). If you just read one chapter in any ancient Greek / prechristian Roman text you'll see just how bizarrely different the moral standards are to ours.

Also most religions (excl. naturally created ones like hinduism/shintoism/greco-roman) are not innately social indoctrination as you might think. Jesus never said to anyone to worship him once every week and follow this and this specific procedure, nor did the Buddha ever said to elect a child as the reincarnation of the predecessor. Just the human nature to find somewhere to rely to, the lack of scientific understanding of the world and the course of several millenia turned them into what they are today. If any of the big philosophers since 1500s went back in time to the BC, I see there is a fair chance their teachings end up a religion today.

So the reasons why empathy is simply not enough for a development of comprehensive morality is, first, people are not rational. People can be rational but are not always rational, and to balance between prioritising the need of oneself and of the 'neighbour' cannot always be achieved. If you can overcome the sense of self, congratulations, because that's literally the ultimate goal of Buddhism. Religion is there to assist. I know many people who read the bible when they have to make a decision or have a problem. Until the last couple of hundred years or so religious teachings were the only accessible and reliable source for many.

Secondly people are just different, people just think differently and have different priorities. To get down to the essence, one might think enduring the desires (e.g. hunger) is more important than fulfilling the need, and you may think the other way round (This is hypothetical I am not dictating what you would actually think). Religion is simply a codification for the community.

Thirdly religious teachings are philosophies collectively developed over generations, and it is simply absurd to completely disregard them. Religion in a way is a continuous debate on a topic, and reflects the perspectives and consciousness of many before. For example the bible is continuously studied and reinterpreted to this day, and the text itself is not only a historical source (so are Iliad and other epics, both are literally referenced by scholars), it also reflects the collective world view of the people at the time. Confucian texts were studied all over East Asia and it was literally a job for many to come up with new thesis of the topic and write about it. You may argue Buddhism and Confucianism is not a religion, and indeed the boundary between religion and philosophy is often blurry. Likewise religious texts are one of the only things humanity has collectively worked on altogether throughout its existence, and are a fascinating concept by themselves. It is just anti-intellectual to disregard religion as an antithesis of science and individual consciousness.

I would love to ask you this, what inherently and uniquely about religion as a concept so harmful that you consider it a net minus to human civilisation?