Answer
The purification comes from remembering Kṛṣṇa—not from the act of drinking wine.
Wine itself has no purifying power. Śrīla Prabhupāda's instruction was a compassionate, individualized method to help one particular conditioned soul gradually become Kṛṣṇa conscious.
It was a special application of spiritual wisdom, not a universal principle.
No previous ācārya presented this as a general practice. It was an exceptional instruction given according to the condition of one individual.
Therefore, this example cannot be generalized.
If Śrīla Prabhupāda personally instructed someone in this way, then following that instruction would purify that particular person because it was the order of the spiritual master.
However, one cannot conclude, "Let us introduce wine into the temple because remembering Kṛṣṇa while drinking purifies us."
That would be a complete misunderstanding.
The eternal principles of devotional service are established through guru, sādhu, and śāstra. These principles are universal and apply to everyone.
Specific instructions given by a realized spiritual master to an individual disciple are applications of those principles, not new principles themselves.
Unless a practice is supported by guru, sādhu, and śāstra, it cannot be accepted as a general rule.
Śrīla Prabhupāda's instruction regarding wine was an act of extraordinary mercy toward one individual whose attachment was so deep that remembrance of Kṛṣṇa had to begin from within that very attachment.
If someone independently imitates this instruction without the direct guidance of a bona fide spiritual master, there is no guarantee that it will have the same purifying effect. It was effective because it was given by a pure devotee under Kṛṣṇa's inspiration, specifically for that person's spiritual elevation.