Considering that Uchihas are basically mini nukes that you planted on your lawn, you can still see that even if the children are clueless about the incident, they might detonate and explode on the village if they ever found out or being manipulated into blowing into the village.
Unlike Sasuke who had to focus on his hatred to his brother, those children might find clues or manipulated into finding the truth would be more likely considering how Uchihas tend to act emotionally than others.
Plus, Itachi might be young and talented but he had to decide between sparing those children(who are likely become those unregulated bombs) or Sasuke(who he can detonate on himself) which he didn't have time to decide considering he was on a limited time limit.
Raven...
the point of killing missing ninja/rogue ninja is to keep the secrets of the clan/village's secret.
So what happens when you leave hundreds of defenseless, brainwash-able, adoptable kids in the middle of a power struggle of multiple clans?
The babies would be cannon fodder, experimented, and harvested for their eyes and genes..
Leaving only 1child(sasuke). Is relatively safe, since they cant poach him under everyone's gaze. Especially since hokage has an obligation to keep the basically ruined clan(uchiha) alive for political reason.
From itachi's PoV, killing the babies are better than them being kidnapped, tortured, experimented, etc. Even if they somehow got protection from the hokage, they'll be excluded and bullied like naruto. Which repeat the hatred of the uchiha's, which itachi desperately wants to end
Considering how Danzo collects their eyes, I think those kids had a better sentence than what Danzo is about to do to them at the very least. I also realize that Uchihas tend to be stalked by creepy old men.
Basically its either the easy way out or how Hitler is doing to the jews. So itachi did the best thing even if its morally wrong. Kinda sad people tend to forget that Uchiha just had the worst fate the moment Tobi put them in a death sentence the moment one Uchiha just poke his bro and crippling him.
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