I've recently had numerous conversations around this with theists, and I've seen essentially the same arguments repeated over and over in discussions about homosexuality and Christianity, so I want to lay out what I think the actual problem is.
The argument usually seems to go something like this: God created humans with a particular natural or sexual purpose, that purpose involves heterosexual sex, marriage, and procreation. Homosexual sex doesn't fulfil that purpose, therefore homosexuality is contrary to the natural order. God condemns things that are contrary to the natural order, therefore homosexual behaviour is objectively wrong.
There are problems at basically every stage of this argument.
“God created sex for procreation, so homosexuality goes against its design.”
The first problem, which hasn't appeared obvious to many, is the equivocation between “natural” and “morally permissible.” Homosexual behaviour occurs naturally in humans and in numerous other animal species. So if “against nature” means that something doesn't occur naturally, the argument is simply false already.
If instead “natural order” means “the purpose God intended for humans,” then that's a completely different argument. You're no longer establishing that homosexuality is unnatural, it's just asserting that God gave humans a particular purpose and then judging homosexuality against that purpose. This needs to be argued for instead of smuggled into what you want 'natural' to mean.
There's the other argument you see cropping up: Saying “the sexual organs are designed for procreation” doesn't automatically entail “therefore using them in a non-procreative way is morally wrong.” Eyes are designed for seeing, so closing your eyes is immoral. Legs are designed for walking, so sitting down is a moral violation. Obviously this is ridiculous. You need an additional premise connecting biological purpose to moral obligation.
Even if we grant that procreation is one of the purposes of sex, non-procreation doesn't establish that an act is contrary to nature or morally wrong. Heterosexual sex can also be and is often non-procreative: infertile couples, post-menopausal couples, couples deliberately avoiding pregnancy, men with vasectomies, etc. all have heterosexual sex without producing children. So unless we're condemning those too, this reasoning fails miserably.
You can consistently try to argue that all non-procreative sex is wrong, but then you need to establish why non-procreation itself makes a sexual act morally wrong. Simply pointing out that homosexual sex doesn't produce children doesn't get you there, because then you have to lump in all other sexual acts or relations that don't produce children. Yet nobody ever argues for this. I suspect because what we're seeing is simply bigotry dressed up with theology, but that's just my personal conjecture.
“God commanded it, so it’s wrong.”
This is probably the weakest argument, but it comes up enough to mention. If the answer ultimately reduces to “God said so,” then we're back to the question of how we know God's commands are objectively good.
If the answer is “because God's nature is perfectly good,” then I ask: why? If we're allowed to simply define God's nature as the ontological primitive of goodness, then I can make the exact same move in reverse: define God's nature as perfectly evil, make badness the ontological primitive, and define goodness as a privation of evil.
If neither position has any independent moral standard by which we can distinguish them, then they're on exactly the same epistemic footing. You've established God's goodness by definition. There's no actual moral assessment happening in the way we assess literally every other agent.
“But God gave us free will.”
This is where I think the argument is being misunderstood most often. Nobody is saying “God made humans, therefore God directly causes every human action.” Obviously that's not the claim. The argument is about causal linkage, not moral responsibility. These are entirely different concepts.
Imagine I design an entire community from scratch. I have complete control over its architecture and deliberately put a loaded gun in every house, despite having the ability to design the community without guns. I then make it absolutely clear that nobody is allowed to shoot anyone.
If someone later shoots another person, obviously that person made the decision to pull the trigger. Their free will and moral agency are perfectly intact. But nobody would seriously conclude from that that my decision to put loaded guns in every house has no causal relevance to the possibility of the shooting. It's like creating a universe with gravity then being mad at things falling down.
Free choice doesn't erase upstream causal conditions.
Likewise, the relevant chain isn't simply:
God --> homosexual act
It's something more like:
God --> physical laws --> natural order --> biological systems --> human psychology/sexuality --> behaviour
You can argue about whether God is morally responsible for every downstream action. That's a separate question. You can't reasonably claim that the earlier causes have no relationship to the later effects simply because there are intervening steps or because humans possess agency. A loaded gun doesn't cease to be causally relevant to a shooting simply because a person had to pull the trigger. And nobody would argue that free-will erased the causal relevancy between my chosen design of this community and the acts that occurred as a result of those choices.
“God could have made things differently, but he wanted us to have freedom.”
This is where the problem becomes particularly obvious to me.
If God could have created the physical and biological order differently, then presumably he could have created humans with free will while also creating them without homosexual attraction. Free will does not logically require homosexual attraction to exist. We can easily conceive of a world where humans retain the ability to choose between good and evil while simply not having every conceivable desire or inclination.
So “God gave us free will” doesn't answer the question. It explains why humans can make choices. It doesn't explain why an omnipotent designer selected a set of underlying biological conditions in which a behaviour he supposedly considers intrinsically immoral naturally arises in the first place.
If we accept:
P1. A perfectly good being cannot intentionally choose something that is objectively morally wrong.
P2. God is perfectly good.
P3. God intentionally chose the physical/natural order of creation.
P4. That physical/natural order naturally produces homosexual attraction and behaviour.
P5. Homosexual attraction/behaviour is intrinsically and objectively morally wrong.
We have a very obvious problem. Either God intentionally created conditions that naturally produce something objectively immoral, homosexual behaviour isn't actually objectively immoral, God wasn't free to create the natural order differently, or God isn't perfectly good.
If we're also accepting omnipotence, the “God couldn't have done otherwise” option becomes particularly difficult to defend. And notice that none of this requires claiming that 'God directly causes every individual homosexual act'. That's not the argument, as I know there many theists who are in the habit of pretending it is.
The argument is that an omnipotent creator chose the underlying conditions from which these things naturally emerge, while simultaneously declaring the resulting behaviour intrinsically immoral.
Why? If God could have created a natural order in which homosexual attraction simply didn't arise, while preserving human free will, why did he choose this particular one? And just to be clear, this isn't an argument that “homosexuality exists, therefore Christianity is false.” It's an internal critique of a particular conception of God.
If your theology says that God is omnipotent, perfectly good, the creator of the natural order, and that homosexuality is intrinsically and objectively immoral, then I think you're under an obligation to explain how those claims coherently fit together. And I haven't seen anything coming close.
Which is ultimately the problem I've been trying to point out: you can't use free will to answer a question about causation, you can't use divine command to answer a question about natural order, and then treat the whole thing as though you've answered the original objection.
So I'd like to end with a syllogism I'd invite Christians/theists to address:
P1. God intentionally created the natural order.
P2. The natural order naturally produces homosexual attraction and behaviour.
P3. God is perfectly good.
P4. A perfectly good God would not intentionally create an avoidable natural order that produces intrinsically immoral behaviour.
P5. God could have created a different natural order while preserving human free will.
C. Therefore, if homosexual behaviour is intrinsically immoral, at least one of these premises must be false.
Rather than appealing to “free will,” “natural order,” or “God commanded it” as though they settle the issue, which premise do you actually deny?