It doesn't seem to me like you're evangelizing a human first leftism. It seems to me like you're reducing a complex argument to "you're celebrating the killing of kids, and you think kids should be killed" you've compared it to the dropping of atomic bombs on two cities.
Again I'd sincerely urge you to read Robespierres arguments against king Louis. It is not a question of punishing an individual, but eradicating a system. Those children existed as parts of that system, and would in most circumstances always exist as that. Pretending like the fear of counter-revolution being fomented once again decades later around the figure of a royal heir as some statistical unlikelyhood, is absurd when we can see exactly that having happened throughout history. As you said yourself there are still bonapartists, orleanists and the like. There's no romanovists. While the orleanists are ridiculous now, they did previously and successfully lead a counter revolution. The bonarparists did as well.
In this sense the fear of the children becoming some later legitimising fixpoint for reaction is not some person "peering into the future", it is us peering into the past. Those children did nothing wrong, but by virtue of the system they were at the top of, they would forever be threats to the USSR. In this way those children were as much a victim of the system as anyone else dying senselessly.