What bothers many people is the issue of Amalek. There are two things to keep in mind. First of all, if their maker tells us to kill them there shouldd be nothing at all wrong with that. Morality dictates the value of life. Life is sanctified by the One who embued it. He tells us to kill them so it is perfectly moral to do so.
It becomes confusing when you are asked, well everybody kills in the name of G-d. The answer is simple: they are all liars. I know that I won’t convince you that we are saying the truth and the others are making it up, but you can agree that if you would know that G-d said to do it, it would be a moral thing to do.
The reason we all want freedom of religion to exist is because no religion is obvious, and history shows that anyone can do whatever he wants in the name of religion. However, in times of open Nissim and Nevua and in the days of Moshiach, when it will be a matter of fact that Hashem rules the world, freedom of religion would make no more sense than freedom of your neighbor’s posessions. Until then, rest assured, we aren’t killing any Amaleikim. Therefore, we will never be violating morality.
The second thing to keep in mind is that in early times a war wasn’t a hired or drafted army fighting its leader’s politics. Everybody, young and old, men and women alike, fought however they can. We see this somewhat in the Palistinian Arabs. The Sefer Hayashar describes how the women of the 7 nations would stand on the roofs and throw things down.
This is besides the fact that one side of the city would be left open for those who wish to escape.
In summary, these things were never carried out when it was not moral to do so.