Of course it matters it was the driving factor behind her decision to take the drug. OP proposed she should have killed them after the drug failed, Ven. responded who would kill their kids because they couldn't feel empathy but that's not why she would kill them is what I was trying to point out with that post.
But she didn't know the drug failed until after their birth, and at that point, she couldn't have aborted them.
While Judge's plan was for them to be cultivated into killing machines, there's no guarantee that would have happened. Sora had two options to prevent that:
1. Administer the drug to counteract the experiment
2. Abort them in the womb
The second one isn't morally right because, again, you can't punish someone over what they COULD do. Otherwise, I could slit your throat right now, say you could have raped someone tomorrow, and call that justice.
The former of the options isn't just more morally correct, it's the only morally correct option because:
1. She isn't sitting back doing nothing to stop the potential of these killing assassins
2. What she's doing isn't punishing them for a crime they haven't even committed yet