O.swald killed L.acie because she had direct access to the Core, threatening the world's stability. So there's the question of why O.swald didn't kill her daughter as soon as he learned that she also had that ability.
One possibility is that, since the Core already obtained a vessel and friend, destroying that vessel and friend would cause greater instability (due to the Core's emotional turmoil) than letting it keep it. Therefore destroying A.lice would be a last resort--something to only do if there's a greater evil (such as Jack). The Core does later release the Will but it's also given companionship after (as planned by Leo) which would ease its emotional pain and therefore lessen instability.
The only other possibility I can think of is simply that O.swald didn't want to go through killing his sister again. So he tried to make everything the same as it was before but without the part where he kills her. This would be in line with what I've noted before, about how the toll of the selfless act of killing L.acie seems to make him more selfish and less responsible after: he's a little more willing to take risks at the expense of the world if it might fulfill some personal emotional desire.
Judging by what happens after his reincarnation--him being unable to kill A.lice or L.acie--you can argue that the latter is a reasonable idea.
However, I have a counterargument to this: he was still much more devoted to his role back then. Even if it would've hurt, he was previously worse in some ways than others, and therefore may still have killed her immediately if not for a reason like the former idea.
In the end, I don't know which it is. From what I remember and can think of at the moment, they're equally likely. Wouldn't L.acie and Levi have considered that he'd kill her for being a dangerous aberration? I feel like I'm forgetting a vital piece of information here that would explain all of this. Like why they wouldn't be afraid he'd just kill her.
