The story of Indra and Vṛtra is metaphorical as explained below.
Since you cited a quote from the Rig Veda. Therefore, in the first place, the question of Viṣṇu helping Indra has to be understood in the context of the primary sources namely Vedas and Brahmanas.
In Śatapatha Brāhmaṇa, it is stated that
वृत्रो ह वा इदं सर्वं वृत्वा शिश्ये । यदिदमन्तरेण ...