Anyways. I think it's many flavours of insane to suggest that any terrible person in history would "stick to his path" no matter what. Nobody is born evil in the real world.
I am sorry but some people are born evil. Now we can argue that how they are raised may change the degree of evil but they will still be at their core evil. Let's get a bit more specific because the word "evil" really is too vague. Evil can often simply mean an opposing will or side in a conflict but when we talk about pure evil we are talking about a sociopath. A person that does not recognize other people as having value, worth and are in capable of empathy for other people. A true sociopath is going to be evil no matter how they are raised because they simply lack the ability to feel other people's emotions.
People are not blank slates. The idea of the baby being innocent is a Christian concept and one that generally serves us well in law and government but in reality is not really true. We can turn the dial up or down but at the end of the day, the song remains the same.
I do agree with you though the "Hitler" baby scenario has a lot more effective solutions than just killing him. That is largely due to the fact as an ordinary person he only had power through other people. The main reason killing Hitler would be a waste of time is not because it would be immoral but that it would not have the desired effect. We overrate the importance of the individual because of own Western framework. Hitler was able to come to power because circumstance of political and economic realities that would still exist if you remove him. The person that would fill is role might not have taken it to the degree of "the final solution" but it would still have likely led to war and something similar.
Let's look at evil on a smaller scale. Rush Limbaugh is a sociopath that doesn't mind making money off the misery of others. If he were to have a stroke and die tomorrow it would not end the thirst that a section of society needs for racist, homophobic and sexist demagoguery. Another "entertainer" would fill that niche just as Rush did as he replaced Morton Downey Jr. after his fall from popularity. The existence of that one person would not change the ugly underbelly of hate in our country. The forces that give people like a megaphone are much larger than any one person. Which actually makes the probably much scarier and problematic than a single villain.
Going back to Apocalypse, the case is very different from Hitler because his power comes from the fact that he is not an ordinary human. So now we have an evil seed with immense individual power. If you combine a sociopath with that much power they would be a threat no matter what and killing them would be the only sane option. Of course in this case, our hero makes the completely inconsistent decision to clone the child and simply repeat history.
The idea that it is wrong for heroes to kill is one that exists only in comic books. It is the one feature that no matter how well a super hero comic is written ultimately stunts the art form because it keeps the morality of the story stuck in childhood.