Its an old and tricky philosophical question - when personal moral feelings and religion conflict, which is the correct path to follow? In Judaism we hold that God, being perfect, gave us our value system through the Torah and therefore any difference between secular and Torah positions means the secular one is wrong.
The problem with this is that it requires a high amount of faith and also a tremendous amount of resistance to the seduction that the surrounding general culture uses on us to pull our souls away from Torah values. For many the conflict is very real and there is a genuine desire to try and accommodate both positions, to be a loyal Torah-observant Jew and a good secular member of society.
We see it with gay marriage, for example. In the non-Orthodox community this is a no-brainer. Almost by definition, Reformatism today sets its moral compass by the values of secular liberalism and then adds in traditional Jewish values only when they don't conflict. On the Chareidi side of the community there is also little debate. The Torah's values rule all and if one has mixed feelings then one is lacking in proper faith.
For those slightly to the left of Chareidism however the picture is not so simple. Exposed to the world in ways that Chareidim often aren't, the perspective on the outside changes. Living amongst Gentiles we quickly learn that most of them are quite decent folk. Many have good senses of propriety, decent and honesty even if their core values diverge from Torah ones. What's more, in many cases it seems their values are superior to ours, for example when it comes to child abuse and protection from pedophiles and abusive husbands. Seeing this can really tug at a person and make him wonder if our system really is the best system.
There are other reasons a person can come to doubt whether halacha and received Jewish values are indeed so perfect. A friend of mine owns an Artscroll book called "What If?" A translation of several teshuvos by Rav Yitchok Zilberstein, it presents various scenarios from daily life in which two Jews come into conflict and need Beis Din to solve it. The format of the book is simple. First the scenario is presented and then the answer. My friend likes to read the scenario and then ask people what they think the right course of action is. Then he reads the official answer, what Rav Zilberstein (or rather, what Rav Eliashiv, zt"l) thinks. What worries me is how many times my answer is diametrically opposed to the official answer.
Why is that? Well, not having an encyclopedic knowledge of Torah my first instinct is to answer the question along the lines of "What would common decency suggest?" or "What would be the best compromise?" This is almost never the right answer, at least according to this book.
All this is my way of explaining why I think that Rabbi Yissachar Katz of YCT wrote his recent post in Times of Israel claiming that our personal moral sense must trump our religious guide. On the surface of it, his thesis is antithetical to Judaism. Our personal moral sense is flawed. Common sense also seems to be in short supply. Who is any of us to put that up against the timeless Divine wisdom of the Torah?
On the other hand, as a prominent Israeli rab recently noted, we live in a strange world where a non-religious teenager expresses more basic Jewish values and behaviour than a Chareidi in full garb, especially when the teenager is trying to express a form of chesed and the Chareidi is lunging at people with a knife trying to kill them in cold blood.
But the situation isn't that simple. The young lady who was murdered at the parade in Yerushalyim might have been demonstrating chesed and was probably everything the glowing eulogies described her as. Her sympathy for her fellow Jew was laudable, her support for a cause that goes against Torah values not as much. A truly decent person who, according to secular standards, was doing a noble deed when she was struck down by a psychotic man.
The murderer, on the other hand, was upholding what he believed were Jewish values. His disapproval of alternative lifestyles, mixed in with his schizophrenia, created a monster with monstrous outcomes. Was he wrong in disapproving of such a parade on the holy streets of Yerushalyim? I don't think many observant Jews, if asked privately for their opinion of such an event, would say that they wish it would happen elsewhere if at all. But to go from that opinion to what he actually did requires a breakdown of all moral sense. In this regard, he was a mirror image of his victim.
Allowing one's moral sense to dictate our religious sensibilities is dangerous. The best example of this is Shaul Hamelech who, as the prequel story to Purim tells us, chose to ignore God's command to totally wipe out the local Amalekite tribes and instead spared the cattle for sacrifice and Agag their king for a separate fate. As the Tanach tells us, he was convinced he was doing the right thing, improving even on God's commands. The result was his downfall into insanity and the loss of his kingship leading Chazal to remind us that those who are kind when God seems to be ordering cruelty will become cruel themselves even when God advises kindness. Therefore Torah must be the compass that guides our moral sense.
If that is the case, then, we must be careful as to how we learn and promulgate that Torah. Being kind doesn't mean accepting things that the Torah forbids or describes in negative terms but it does mean keeping a level head when dealing with proponents of those things, treating them as fellow human beings and Jews with all the respect that warrants. Hate the sin, not the sinner as the Gemara tells us. It means disagreeing and holding to the proper position without rudeness or self-righteousness. It is most difficult since emotions can often cloud proper judgement or lead one onto a dark path that is illuminated by an illusory light. It the difficulty that comes with following a true Torah path but the one that brings us closer to the Creator. Ultimately it does demand that we mold, or at least subordinate, our moral sense to the Torah through proper understanding that learning should bring.