you should be able to go back to sector space. set up your mission so it goes space->space and just change whole map to the sector space door you want from the transition box that appears on the story board.
I tried doing that with a transport mission i was working on. I was only able to be dropped into sector space on the first map transition. All subsequent transitions would not give me the option of selecting the sector space door, it only would allow me to select the maps I had created.