Even though the duskrtis, or miscreants, are annihilated, this is ultimately good for them
SB Canto 10.1 to 10.13
O Lord, You are always in full knowledge, and to bring all good fortune to all living entities, You appear in different incarnations, all of them transcendental to the material creation. When You appear in these incarnations, You are pleasing to the pious and religious devotees, but for nondevotees You are the annihilator.
This verse explains why the Supreme Personality of Godhead appears as an incarnation again and again. The incarnations of the Supreme Personality of Godhead all function differently, but their main purpose is paritrāṇāya sādhūnāṁ vināśāya ca duṣkṛtām (BG 4.8)—to protect the devotees and annihilate the miscreants. Yet even though the duṣkṛtīs, or miscreants, are annihilated, this is ultimately good for them.