The Quran is not saying, "Christians believe God had sexual intercourse." It is saying that any real divine "child" is impossible for God, and 6:101 uses the absence of a spouse as one clear way to expose the absurdity of literal offspring-language when applied to the Creator.
The criticism at its strongest
The objection deserves to be stated fairly. Christian theology, especially in its Nicene form, does not teach that Jesus is God's son through biological procreation. "Son" is used for an eternal relation: the Son is "begotten, not made," sharing the divine nature, while the virgin birth involves no human father and no divine wife. So, the critic says, when the Quran argues, "How could He have a son when He has no wife?", it seems to attack a crude belief Christians do not hold.
"Originator of the heavens and the earth. How could He have a child when He has no companion? He created all things, and He is Knowing of all things."
Quran 6:101
What the verse is actually targeting
The key word in the verse is "walad" - child, offspring. In normal Arabic usage, this is not an abstract philosophical term. It carries the sense of derivation, lineage, and origination from another. The Quran's point is not that every claimant to divine sonship imagines a divine marriage-bed. Rather, it is asking: if you mean a real child, then the idea is already incoherent, because offspring belongs to the world of pairs, species, bodies, dependence, and generation. God is not within that order at all.
Classical commentators read the verse this way. The mention of a "companion" or spouse is not a report that Christians must believe in a heavenly wife; it is a rational argument against taking "child" seriously of God. Al-Razi, for example, treats divine offspring as impossible because it would imply likeness, composition, need, change, or belonging to a genus. Al-Tabari likewise explains that created beings have offspring through causes and partners, while the Creator is beyond that.
The Quran also rejects the refined doctrine
The Quran does not only answer a crude biological version. It repeatedly denies that God begets, is begotten, shares divinity, or is one member within a differentiated Godhead. That reaches beyond sexual procreation and touches the heart of Nicene language too.
"He neither begets nor is begotten."
Quran 112:3
"So believe in Allah and His messengers, and do not say, 'Three.' Stop - it is better for you. Allah is only One God. Glory be to Him above having a child."
Quran 4:171
So if a Christian says, "We do not mean biological sonship," the Quranic answer is: that removes one crude meaning, but it does not solve the deeper problem. If "Son" means a second divine person who shares God's essence, the Quran rejects that as compromising absolute divine oneness. If it means a created servant loved by God, then Islam accepts the honor but rejects the word "son" because revelation reserves divinity, worship, and eternal self-existence for Allah alone.
What this does and does not prove
The objection proves, at most, that Quran 6:101 should not be read as a full technical summary of Nicene theology. Muslims need not claim that mainstream Christians teach God took a wife.
But it does not prove the Quran misunderstood Christianity. The verse is a concise argument against real divine offspring, using ordinary language and its implications. The wider Quran then addresses the more developed claim that Jesus shares in divinity. Its disagreement with Christian doctrine is not based on thinking Christians believe in sexual reproduction; it is based on a stricter account of God's oneness, self-sufficiency, and transcendence.
In plain terms: the Quran is not refuting a doctrine no one holds. It is rejecting the whole category of divine sonship, from its crudest form to its most sophisticated theological form.