Answer
You have to understand this carefully. You and I can also go back to Godhead if we are surrendered to Kṛṣṇa and chanting His holy name at the time of death. But suppose I say, “I want to help you go back to Godhead. Please chant Kṛṣṇa’s holy name, and I’ll cut your throat.” Would that be the right way to help you? Of course not.
Giving pain to another person — especially to a Vaiṣṇava — is not the proper way to liberate him. The fact is that Vṛtrāsura was already an exalted, pure devotee. After his death he would naturally return to Godhead. Vṛtrāsura himself knew this, and that is why he was eager to fight with Indra. He understood that Lord Viṣṇu had already declared that the vajra would kill him. He thought, “Because of my offense at the lotus feet of Lord Śiva, I have received this asura body. Now that will be finished, the offense will be cleared, and I will return to the lotus feet of Saṅkarṣaṇa.”
He even expressed this while speaking to Indra. He said that he desired to die and become the servant of the servant (dāsa-dāsānudāsa). That was his intense aspiration. Therefore he urged Indra: “Take up your vajra and kill me.”
When Indra heard these words — that Vṛtrāsura wanted to become the servant of the servant — he realized the exalted position of Vṛtrāsura. “He is a greater devotee than I am. How can I kill him? I should not commit this offense.” Thus Indra became reluctant and unwilling to fight.
When Vṛtrāsura saw that Indra was hesitant, he attacked him, forcing Indra to defend himself. In this way, Indra was compelled to fight, and unwillingly he killed Vṛtrāsura.
Although, by Indra’s action, Vṛtrāsura ultimately went back to Godhead, from Indra’s side he still inflicted pain and acted inimically toward a pure devotee. Therefore he had to face the reaction. That is how we should understand it.
We can help another devotee go back to Godhead, but not by acting inimically toward him. Real para-upakāra means helping others spiritually, not harming them. Indra acted inimically toward Vṛtrāsura, and that constituted an offense. He understood this himself; that is why, even though all the demigods were happy after the victory, Indra remained unhappy.