If they weren't still enemies things would have probably been different. If they were repentant they would have been forgiven, but they weren't. They were still enemies. So it remains, if a few had to perish so that all man kind could have salvation then that would be just.
I see your points though, if you don't believe in God or that he is all knowing. If he didn't know those babies would grow up to be enemies and still present a threat to salvation then that god would be an evil tyrant. However, if he is all knowing, and just and had to do something to ensure we had salvation and that was the only option then it would be just.