Next time send me here: http://www.chabad.org/library/article_cdo/aid/267677/jewish/Wipe-Out-Amalek-Today.htm
and
http://www.chabad.org/library/article_cdo/aid/2494730/jewish/Torah-and-Genocide-FAQ.htm
That take is distinctly apologetic. It may be a valid explanation (one would need early Talmudic sources for the allegorising of Amalek) but it is definitely not the mainstream approach.
Jews pray daily for the Final Redemption which will be accompanied by the return of kingship and prophesy to the Jewish People. In those days G-d's glory will be know to all the nations of the world and no one will think to question His commandments because of apparent inconsistencies with western morals. Until then, Jews raised in western democracies in the 21st century will likely have issues understanding certain commandments that seem cruel and immoral to them. To those with an proper appreciation of their Tradition and Heritage these issues will not be disturbing. We know that a day will come when we will no longer have these issues.
In regards to Amalek, being that we have no way of identifying them if they do exist, we are exempt from our obligations in relation to them. If in the time of the Final Redemption we become aware of Amalek's continued existence, we will be obligated to carry out our obligations relating to them including the killing of women and children. In that future time it will be evident to all that that is not immoral.
