Joseph:
http://www.chabad.org/library/article_cdo/aid/267677/jewish/Wipe-Out-Amalek-Today.htm
See this article for a different perspective on killing Amalek today. (From Chabad, no less!)
Anyway, the situation is not as black-and-white as you paint it. For one thing, the obligation to destroy Amalek is cultural rather than national, as is clear from the Rambam which states that we are only to kill them if they refuse to accept the Sheva Mitzvot Bnei Noach.
http://dir.salon.com/story/books/int/2005/11/10/karpinski/index.html
If you look at this article, you will see that an estimated 90% of the Abu Ghraib prisoners were actually innocent. Do you call that “good reason” to torture them?