It strikes me that the simplest way to follow Brandon’s advice in a debate with Craig would be to compare the divine command to slaughter the Amalekites to two other commands to destroy cities given to righteous men: the destruction of Sodom proposed to Abraham; and the destruction of the Israelites proposed to Moses on the mount. In light of these, it seems that the righteous response to God telling you about the slaughter of a whole people is to plead with him to be mindful of his mercy, and to persevere in this until he relents. So far as Israel alwasy had an obligation to follow the righteous example of its patriarchs, the call to intercede for those who are (justifiably) doomed is a true obligation, and to fail in this obligation is a serious fault. Notice that this obligation is more directly based on the literal sense of Scripture more than Craig’s divine command literalism – it is exactly how Saul would have responded to the command if he took the literal sense of scripture as his guide in life.
On this account, the real failure of the Amalekite massacre is that Israel fails to extend the mercy of God to the nations. They choose to be simply like the other nations, and perform a rather typical action of a conquering army. The Amalekite massacre is really a failure of Israel to “let God be their king” and instead to just “have a king like other nations”. If God were their king, as he was for Abraham and Moses, the Israelites would have been true to their obligation, which has always been to be a conduit of mercy to all nations.