I just started reading this paper, and so far it's interesting: Avi Sagi, "The Punishment of Amalek in Jewish Tradition: Coping with the Moral Problem," Harvard Theological Review 87, no. 3 (July 1994): 323-46. If you have access to JSTOR, you can download a copy. If you don't, you can send me an e-mail and I may be able to arrange for a pdf of it to appear in your in box.
In all too many Orthodox synagogues, Parashat Zakhor is an opportunity for a Fifteen-Minute Hate. I don't know how most non-Ortho 'gogs handle it. Some of them may just ignore it. This paper avoids both.