I voted for "morally the same" because of the overlap of both concepts. You can put either in a "better" light than the other.
For instance, I could argue that, if I KNEW that my neighbour was a child molester and child murderer (because I saw, heard... ) him do so, but because of one or other reason, justice didn't accept my charges and the man went free, and I decide to kill him to prevent him from continuing (even if that means that I will go to jail or worse), then this "assassination" is almost a nobel act.
But I could also decide to, say, kill all Jews because I am convinced that they are the evil of the world (innocent example of course

), in which case I'd think that such an assassination, when I do it on large scale (say, 6 million people), would be very bad.
Now, if we go to "terrorism", terrorism is a notion that can go in different directions. At its core, terrorism is the act of scaring the hell out of a population by violent acts, in order to obtain from that population that they exert pressure on their political system to take certain decisions. So you need an agenda, and acts that cause terror amongst the population in such a way that we get closer to the execution of the agenda. This can be by killing randomly some people (that's indeed scaring a population), but it does not necessarily go through the act of killing. For instance, sending some white powder around the country can act just as well in that way than to blow up a bomb.
Now, imagine that a group of terrorists uses such methods, say, to get a population rise up against their evil dictator who is assassinating others. What's then morally on the higher ground ?
The preference most people give here to assassination over terrorism is simply given by the current psychose over terrorism spread by some western politicians: they compare the murder of the lover of your wife to the twin towers, and say that if they have to choose, they'll go for the murderer over Ben Laden. It's one half guilty victim over 3 or 4 thousand innocents. But murder can be on a large scale, and terrorism can have a "good" agenda too.
Do you also prefer the systematic murder of the 6 million Jews over the hypothetical 20 victims of a terror group that wants to get rid of, say, Fidel Castro ?