Curious I feel this is bug but almost looks like it was designed this way.
I started my mission by using the DS9 and Wormhole map built it up, but when I tried to send you to DS9 from the main contact I can't!

In the Beta Ursae every system is selectable except DS9 or Bajor

I'm trying to make a mission that takes place in orbit around Bajor, but you can't select Bajor as an entrance from Sector Space.. So I'd like it as well.

they do need to add bajor and ds9 to the door list. at the very least bajor as most people would associate ds9 with bajor

It is possible to use the real ds9 as a start point though. drop an 'add contact' to the beginning of the story line and then select one of the available characters from ds9. you can then exit via one of the cargo bay doors as your first door transition (just make it clear to the players which one to use) then you can switch to one of the pre created ds9 maps and go from there. its not ideal but it works.