Hail the freighter and tell it where you want it to go. Its actually that simple, and yet, can be broken down as follows (and seem overly complex):
Target freighter
select communications tab - you should see something like "change course" and "disengage"
-under "change course" you have 2 of 3 options, "Def Satellite", "Minelayer" and "Planet". You won't have the option to select the destination you are going to already, but the other two will be available.
-selecting disengage will have the freighter go to the nearest exit. If you have a tractor on the freighter be sure to rotate the freighter behind you so you hit the magic red line before the freighter. If the freighter leaves before you do, even if you are microseconds away from warping out yourself, you die.
Hope that helps!
**Highly recommend you play this from the ISC side, when you are done with your current campaign of course. It makes for a very interesting change
**