This is a common complaint among atheists. But it is all governed by science - in essence, free will. If water boiled at 212 degrees on a random basis without rules to understand, an even harsher reality would have been created. Science is free will with plainly laid out rules for humans to understand. This is much more merciful than creating a chaotic universe that has no discernible pattern for human understanding.
This includes the biology of the brain, which can lead some to murder and mayhem. We don't understand the brain well today, but that doesn't change the fact that its construct is one of pure, understandable science.
"…when we realized we're all alone in the universe, as far as we can tell from a rational understanding of the evidence?"
A rational understanding of the evidence contradicts this. Statistically speaking, given recent discoveries regarding exoplanets in our one small galaxy alone (disregarding the billions of others), the chances that there is not additional sentient life is nil.
Many Christians are resistant to the idea that there can be vast populations of other sentient beings because humanity is supposed to be special, according to some biblical interpretation, but that interpretation isn't supported by any actual biblical verse, and the false interpretation defies science just as the creation story does (there are alternative creation stories in non-canonical texts, but they didn't make the cut).
To your overall point that Paul's epistles are a mess, I agree. And it actually does go to core problems with Christianity.
Patriarchal authoritarians conquered the Christian church by the third century. Patriarchs established biblical canon, then claimed that the entirety of the Bible is the indisputable word of God.
They created their canon while actively suppressing, for example, the Gospel of Mary and other scrolls that contradicted their rule of order. Canon was, then, whatever the patriarchs running the clerical fiefdoms said it was.
I question whether all of Paul's epistles were even fully written by him. Consider his statement from 1 Corinthians 14: "As in the churches of the saints, the women should keep silent in the churches. For they are not permitted to speak, but should be in submission, as the Law also says. If there is anything they desire to learn, let them ask their husbands at home. For it is shameful for a woman to speak in church."
Huh? Dude, you had multiple female deacons. Did you put duct tape over their mouths? Besides, Jesus said, "Dump the Law. I have a new one for you."
Paul himself refers to female deacons: "I commend to you our sister Phoebe, a servant of the church at Cenchreae, that you may welcome her in the Lord in a way worthy of the saints, and help her in whatever she may need from you, for she has been a patron of many and of myself as well" - Romans 16:1–2
He doesn't then go on to say, for the sake of consistency, "but don't listen to a word she says, and in fact, if she speaks, send her home to bake bread."
Anyone who has done significant reading and writing will also notice a strange segue within 1 Corinthians 14:26–40. He's discussing the nature of God, "For God is not a God of confusion but of peace." and then starts complaining about women, almost as a bizarre afterthought.
I would argue that much of Paul's writing was tampered with by patriarchal scribes for the convenience of agenda. Christian clerics would call such a claim blaspheme, but it is inconceivable that the writings did not suffer numerous alterations during the multiple translations and transcriptions within what was by any definition a misogynist society.
Corinthians' target market, in particular, was a patriarchal society that banned women from the priesthood. Did Paul adapt his teachings to the locals or did a scribe inject the hostile treatment of women? Either way, the notion that women should keep their mouths shut is inconsistent with the realities of Paul's ministry and early Christianity.
Acts 18:26 not only reports on Priscilla ministering to men but correcting one, Apollos, who himself was a preacher in those early days.
One could even argue that Mary Magdalene was Jesus' most significant apostle. He relied on her to spread the word and said to her just after his resurrection:
"Go to my brothers and say to them, I am ascending to my Father and your Father, to my God and your God." (John 20:17)
The story of Mary Magdalene was so corrupted by patriarchs that most people still believe she was a prostitute. She was not. But even if she had been (again, she was not), the Bible is clear that Jesus held warm regard for prostitutes, for whatever reason.
Christian Gnosticism, which pretty much held sway for the first couple centuries, when women played huge roles in early church services, focused on the individual pursuit of the spiritual realm before male church leaders took control and restricted Bible reading to clerics and redirected their constituents to a Leviticus mentality.
Martin Luther's corrections to this were minor - protestants still thumped their chests about specific rules and laws, including homosexuality, all things that Jesus specifically said to chill out about. The message was, "go ahead and read the Bible, but don't be Gay about it."
Evidence from the Nag Hammadi indicates a much stronger tendency towards the pursuit of individual spirituality than Paul's epistles. For example, The Gospel of Thomas reads more like "A Course in Miracles" than it does the patriarchal rule of law found in canonical gospels. Same with the Gospel of Mary (which, if not written by Mary Magdalene, was probably at least based on her devotions and life).
Jesus was only concerned with one thing: appreciate the nature of love (God), and treat people accordingly. That was really the whole of his ministry. Humans promptly corrupted his message. It remains corrupted to this day.
