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Bhaktivedanta Narayana Gosvami
From the book “Sri Vraja-maṇḍala-parikramā”:
Indra, the king of the demigods, had committed an offence at the lotus feet of Śrī Kṛṣṇa and the Vrajavāsīs, and was therefore an offender. He worshipped Śrī Kṛṣṇa at this place to seek for forgiveness. One name of Indra is Śakra, from which the name Śakaroyā is derived. Indra’s place of worship thus became known as Śakaroyā.
Rajashekhara Dasa
From the book “Chaurasi-kosa Vraja Mandala Parikrama”:
This place was known in ancient times as Sakrasthana or sometimes as Sakaroya which is derived from Sakra, one of the names of Lord Indra, the King of heaven. The Bhakti-ratnakara says, “Sakrasthana was later named Sakaroya. This place is famous because it was here that Sakra (Indra) became afraid after causing the terrible rain in Vraja.” After having caused a devastating flood in Vrindavana, Lord Indra was surveying the scene of destruction in this region of Vraja while remaining concealed within the clouds. Indra became fearful due to his mistake of trying to punish the Vrajavasis, simply because they had stopped the performance of the Indra-yajna. After Krishna lifted Govardhana Hill and saved all the Vrajavasis from the torrential rain, Indra felt totally defeated and realized that Krishna was in fact the Supreme Personality of Godhead. Thus he became fearful and full of remorse thinking that his actions were highly offensive to the lotus feet of the Lord.