The objection identifies genuine historical questions, but its conclusion is stronger than its evidence. The Kaaba's later use by pagan Arabs does not by itself show that the sanctuary began as a pagan shrine, and Islamic sources explicitly describe that later paganism as a corruption of an older Abrahamic foundation.
What the objection fairly establishes
The Kaaba was a cube-shaped sanctuary in pre-Islamic Arabia, and Arab pagans placed idols in and around it. Other Arabian sanctuaries also existed, including Dhu al-Khalasa, which some sources call a "Kaaba" and which the Prophet Muhammad (PBUH) ordered destroyed. The Bible does not mention Mecca or the Kaaba, and the surviving external evidence connecting it with Abraham is limited. It is therefore reasonable to ask whether the Islamic account is a later religious explanation of a pre-Islamic shrine.
That is a serious historical question. But several different claims are being joined together: that the Kaaba was cubic, that pagans used it, that other shrines were called kaabas, and that early external evidence is scarce. None of these facts, by itself or together, proves a pagan origin.
What the Quran actually claims
The Quran does not deny that the Kaaba was surrounded by pagan practices. It says that Abraham and Ishmael established the House and prayed that it be kept pure for worship. It also describes the sanctuary as an ancient center of pilgrimage:
"And [mention] when Abraham was raising the foundations of the House and [with him] Ishmael, [saying], 'Our Lord, accept [this] from us. Indeed You are the Hearing, the Knowing.'"
Quran 2:127
On this account, Abraham did not invent every later custom found at the site. Rather, a monotheistic sanctuary was later filled with idols, just as prophets in other societies confronted the corruption of earlier revelation. The existence of religious misuse is not evidence that the original institution had the same purpose.
The Quran also says that the first House appointed for humanity was at Bakkah, "blessed and a guidance for the worlds" (Quran 3:96). Whether one accepts that claim depends partly on accepting the Quran's revelation, but it is not accurate to say that Islam quietly borrowed a pagan shrine while offering no account of its earlier history. Its account is explicit and consistent.
Why the rituals are not stone worship
A cube is a simple and stable architectural form; its use in several sanctuaries does not establish a shared theological origin. Likewise, circumambulation is not inherently pagan. It is an act of worship whose meaning depends on whom the worshipper intends to worship.
The Black Stone is not treated as a deity or as a source of independent power. Umar ibn al-Khattab famously addressed it, saying that he knew it was only a stone and that he would not have kissed it had he not seen the Prophet Muhammad (PBUH) do so. The rite is therefore symbolic obedience, not veneration of a god.
Dhu al-Khalasa shows that rival pagan shrines existed; it does not show that the Kaaba originated as one. The evidence establishes pagan occupation and later competition, but it does not disprove the Abrahamic origin preserved by the Quran.