In light of some recent discussions, I thought I'd repost some tentative thoughts on the subject (based on a 2005 post of mine), and see what the rest of you think.
1. Morality: Government-sponsored assassination is essentially an act of war; it's an attempt to affect another nation's government policy by military force. Nonetheless, if an invasion is morally justified, it seems to me that an assassination is if anything more so. It would be an odd morality that allowed the killing of enemy soldiers, many of whom are personally morally innocent, but forbade the killing of their commander-in-chief—or even ostensibly civilian leaders of the enemy government—who may be morally culpable indeed.
Idi Amin was ultimately driven from power by a Tanzanian invasion (which was prompted by a Ugandan invasion of Tanzania, but would have been eminently justified even without that). If the Tanzanians or others could have stopped Amin's murders by assassinating Amin, and without killing any Ugandan soldiers, that would have been even better.