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 द्यावापृथिवी स यदेदं सर्वं वृत्वा शिश्ये तस्माद्वृत्रो नाम — १.१.३.[४] vṛtro ha vā idaṃ sarvaṃ vṛtvā śiśye yadidamantareṇa dyāvāpṛthivī sa yadedaṃ sarvaṃ vṛtvā śiśye tasmādvṛtro nāma 1.1.3.[4]
In ancient time Vṛtra was sleeping covering the entire world specially the earth and the heaven. As because he slept covering these all, therefore he is named after Vṛtra. √vr to cover. In this connection the derivation from Yāska’s Nirukta (2.16). Yāska derives Vṛtra as follows,
तस्मात् इन्द्रशत्रुः । तत् कः वृत्रः । तत् आभिवादिनी एषा ऋक् भवति । [त्वाष्ट्रः असुरः इति ऐतिहासिकाः ।] अपां च ज्योतिषः च मिश्रीभावकर्मणः वर्षकर्म जायते ।
तत्र उपमार्थेन युद्धवर्णाः भवन्ति । अहिवत् तु खलु मन्त्रवर्णाः ब्रामन्णवादाः च ।
तस्मिन् हते प्रसस्यन्दिरे आपः । विवृद्ध्या शरीरस्य स्रोतांसि निवारयां चकार ।
अतिष्ठन्तीनाम् अनिविशमानानाम् इति अस्थावराणां काष्ठानां मध्ये निहितं शरीरं मेघः ।
इन्द्रशत्रुः इद्रः अस्य शमयिता वा शातयिता वा । वृत्रस्य निण्यं वि चरन्ति आपः दीर्घं तमः आ अशयत् इन्द्रशत्रुः । मेघः इति नैरुक्ताः । शरीरं शृणातेः । शम्नातेः वा ।
वृत्रस्य [ निण्यम् ] निर्णामं विचरन्ति विजानन्ति आपः इति । दीर्घं द्राघतेः ।
तमः तनोतेः । आशयत् आशेतेः । अतिष्ठन्तीनाम् अनिवेशनानां काष्ठानां मध्ये निहितं शरीरम् ।२.१६ ।
Purana says that he is a demon born of but the authors of Nirukta hold that he is nothing but cloud. Sāyana supports the opinion. He says that the root √vr. to cover seems to be quite appropriate. Lightning and clouds combine to produce rain and that interaction of lightning and cloud is described in the simile of the battle between Indra and Vṛtra. After killing Vṛtra, Indra was known by the title of Vṛtraghna. References to this struggle are to be found in many places in this Brāhmaṇa e.g., I.2.4.1, I.6.2.3, II.5.3.18, II.5.4.I, II.5.4.9, II.6.I.I, and IV.I.3.1
Indra-Vṛtra (Śat Br. 11–5–3–18)
It is said that in the context of Sākamedha offerings Indra slew Vṛtra. It is by means of all the seasonal sacrifices, that the god slew Vṛtra. The sacrificer invited Indra to make a bull roar in the Sākamedha offerings. The sound is known as Vaṣat. For the bull is indeed Indra’s form, etad vā idindrasya rūpam yadṛṣabhah.
Indra-Vṛtra (Śat Br. II-5–4–1)
The Mahahavis or great oblation is an integral part of the Sākamedha. By means of the great oblation Indra slew Vṛtra. So the sacrificer thereby slays his wicked, spiteful enemy and gain the victory by performing this seasonal sacrifice.
Indra-Vṛtra (Śat. Br. II-5–4–9)
Before the slaying of Vṛtra, he was indeed Indra, but after the slaying of Vṛtra, he became Mahendra even as a king becomes a Maharaja after obtaining victory. For this reason, a rice pap is offered to Mahendra i.e. Indra.
Hence, the help of Viṣṇu, based on the primary sources, is to be understood in the context of providing the environment to Indra for slaying the Vṛtra.
P.S.: Below an explanation is provided to clarify the word "leagued".
Visnu is a friend of Indra, with whom he is frequently allied in the fight with Vṛtra. RV.VI.69 is dedicated to the two deities conjointly and that Indra's name is coupled with that of Viṣṇu in the dual. Viṣṇu is Indra's intimate friend RV.I.22.19. विष्णोः कर्माणि पश्यत यतो व्रतानि पस्पशे । इन्द्रस्य युज्यः सखा ॥१९॥
Furthermore, verses 4 to 6 of the 99th Sukta of the 7th Mandla are attributed to both Indra and Vishnu. Therein it is stated that: उरुं यज्ञाय चक्रथुरु लोकं जनयन्ता सूर्यमुषासमग्निम्That is Indra and Vishnu generates Surya, Usha and Agni. This is an indication to "league".
