Religious morality is not morality. It's often just evil, cruelty, and contempt for others wrapped up in a pretty facade. A piece of shit spray painted gold. It's why "There is no hate like Christian Love." (which I like to broaden to Religious Love) is a saying. Religious people don't stop having those thoughts, and atheists don't automatically have them.
Religion loves to ignore and reject reality, biology is reality. You're 100% right about genetic makeup and Nature vs Nurture stuff.
It kind of gets into the topic of Free Will (which doesn't exist) and whether or not we should hold people accountable for their actions if there is no free will. We need to to maintain a functioning society, of course... so I would turn the direction of the discussion towards imprisonment vs death penalty vs rehabilitation. There are ample amounts of evidence proving that rehabilitation works... but only for some types of crimes. Some people are repeat offenders and never stop no matter how many times they are punished. Some crimes are so severe that maybe they should never be forgiven... but people make mistakes, drugs, mental health, physical health (in ways we still don't fully understand) can all cause people to "lose their minds/lose themselves" and how do we differentiate between those people and people who did something in a sober state?
It's all so blurry and grey and I don't even know how to approach all of it.
Personally, I think having lots of horrible thoughts and choosing never to act on them makes you a better person than someone who was born with a silver spoon in their mouth and the perfect conditions while they were being raised.
The Damn Commandments have FUCKING THOUGHT CRIME IN THEM AS A FORBIDDEN ACT.... ARE WE FUCKING KIDDING????? (that's not even to mention the other problems with them like the lack of prohibition of slavery and the tenets of narcissistic deity worship.) Like, there are popular movies out there all about thought crime and how evil of a concept it is... yet these "good, moral, upstanding, better than everyone else" religious fucking shitheads think thought crime is real and deserves INFINITE ETERNAL FIERY PUNISHMENT....... Nobody who thinks that kind of shit is a good person, regardless of what they refrain from doing. Same thing for one of the most evil concepts invented by man... "hate the sin, lover the sinner." They use this to maintain the belief that gay people are evil, choose to be that way, and deserve infinite eternal fiery punishment. They reject basic human compassion, empathy, and they also reject reality. They think that certain people deserve unimaginable suffering BECAUSE OF THE WAY THEY WERE FUCKING BORN.... that is the epitome of evil. They think being gay is thought crime against their holy narcissist. Their "love" is bullying, demeaning, harassing, and maybe even assaulting gay people until they "choose to be straight" so they "can get into heaven." If you ask me, they need to read their stupid shitty book of immorality and see one of the few good parts in it where it says "You [God] knit us together in our mother's womb, you create our inmost being." which means that, by their own beliefs, God made everyone exactly how he wanted them to be. They say God gives people tests, and tests his "strongest soldiers" so to me, trans people being born in the wrong body and having to struggle internally and be mistreated or worse by the people and world around them is a test. A test that his believers almost all fail. Instead of showing kindness, empathy, love, and acceptance... they reject God's will and reject people based on the way they were born.
Religion doesn't make you a better person, if often makes you a worse person. Religious morality isn't morality, it's thinly veiled immorality that functions mostly off of brainwashing and gas lighting. Having no bad thoughts doesn't make you a good person. Not acting on bad thoughts makes you a good person.
We cannot control the thoughts we have, we can control how we act on them though. That's why thought crime is one of the most evil and recognized as evil concepts in all of human existence. It feels like yet another way, especially for the religious, to target people with poor mental health and declare them as less of a human being. Religious people would rather physically torture a mentally ill or neuro divergent person for "being possessed by a demon" than they would should kindness, empathy, and care for that person. Sorry, I'm fucking angry today, and I'm sickened by how destructive religion is to literally everything... especially the human mind. It sickens me more than I could ever properly put into words. I watched a childhood friend of mind go from a curious and opened-minded person to someone completely captured by Christian Nationalism and White Supremacy as we became adults. It makes me so fucking sick and so fucking angry. I always thought he was a smart person. I thought he was a decent person.
Coming to grips with how bad so many "good", or supposed to be good, things and people are as far from good as you can get was really difficult. I remember coming to terms with accepting how shitty and awful both my parents were in every way. It was devastating.
Also, the ability to resist temptation is a sign of strength, or quality of character, or discipline. Maybe even a mix of them or all three. Kind of reminds me of the saying that goes something like, "You're not weak because you can't handle something, you're strong for handling it for so long." It is very human, and very much a trait of biological organisms, to be tempted and to give into temptation. As animals that are intelligent as we are, it comes down to making a choice and refusing to make choices that cause harm to others. Being tempted into eating an extra cookie doesn't matter. Being tempted to steal someone else's cookie with their name on it in the communal refrigerator because you really want one is not a good thing, but choosing to go ahead and steal it is the problem and the only thing that matters.
We cannot control our thoughts, our thoughts do not make us who we are, our actions do.