Only half the assasinations missions work out this way. It is shamefully poorly written as a mission though.
Somewhat less than half I would say, a pretty small percentage have this wrinkle. That said, I agree it is poorly thought through...
The problem with most wrinkles that FD have inserted into the mission system, in order presumably to add some excitement or challenge into what may be perceived as rather dull missions is that most of the time the wrinkle doesn't insert anything new. It just has you repeat steps that you did only moments before. This particular wrinkle is particularly bad for that, as most of the time, the informant simply sends you back where you just came from and has you repeat the scan of the nav beacon again.
While people do say they have been sent to different systems, which might give at least the hint of a chase flavour, I have had many of these wrinkles over time, and have always been sent back to the original target system.