Take a sufficiently satisfying object type like units, give it the locust (Aloc) ability, so you cannot click it anymore. Disable its attack, behavior etc., so it does not have disturbing side effects. Create an instance of this object when the missile is launched, start a repeated timer running a function that moves the missile bit by bit in the way you want, the timer's interval being the temporary differential. Everything else is maths.
For the linear movement from A to B you can divide the x/y/z difference by the travel duration and then multiply it by the interval to gain the xAdd/yAdd/zAdd per timer call. To gain the coordinates at a distance and angle from a source spot in R², you can use polar projection targetX = sourceX + dist * Cos(angle), targetY = sourceY + dist * Sin(angle).
After the duration or you may record the travel length too, or whatever the cancel condition is, halt the missile, destroy timer etc.