Good or bad omen depends on how one interprets a source of inspiration. The owl inspired Ashwatthama to commit treachery in the darkness of the night. Kripa soiled his hands with that sin. They remained immortals to lick their wounds and suffer their sins.
Also, Krishna did not avert the killings of Dhrishtadhyumna and Shikhandi because their roles were done. Even though Draupadi was his friend, he knew ho ambitious she was and how she was inwardly jealous of Abhimanyu. Arjuna was Krishna's favorite hence he ensured in his way to protect and promote Arjuna's grandson Parikshit as the next king.
History has it that as he killed Draupadi's five sons, Ashwatthama falsely believed that he actually killed the five Pandavas. That made the Kauravas a bit off guard for the next day's battle.