There is a subtle difference, although the meanings of the two words overlap. Assassination is (arguably) murder, even if the assassin or those behind him seek to justify it in the name of a particular cause, be it political, religious, revenge or whatever. It might be murder to some but not to others, depending on who the victim is and the circumstances around it. Aside from the legal definitions of murder, the word usually implies a killing that is both deliberate and morally wrong. However, where does one draw the line between a deliberate killing (other than in self defence) which is justified and one which is not justified? This brings up the whole subject of the morality of killing in war, judicial killings (execution), or assassinations sanctioned by states or other entities such as factions or terrorist movements. A pacifist would say an assassination is always tantamount to murder. Non-pacifists, however, who agree with or support the reason behind the killing might not be willing to view it as such. A very interesting moral debate. Anyone know of any writers on the subject?
The Concise Oxford English Dictionary defines assassinate as to murder (a political or religious leader). This seems vague though I suppose it fits in with everyday usage. Interestingly it says that the word assassin also refers to ''a member of the fanatical Nizari branch of Ismaili Muslims dominant at the time of the Crusades'', the word originating in the 16th Century. It can be traced back to French, Latin and, interestingly, Arabic (''hasisi, meaning hashish-eater, referring to the Assassins' reputed use of hashish before murder missions'').