You can however finish the Juhani sidequest after you trigger the premium items quest. What you need to do -
Talk to Juhani on the Ebon Hawk as much as you can, and use her very sparingly, as RH advised - only bring her into an area far away from the EH. Once you get through the Leviathan, go to Korriban, get the premium item trigger started, and then you can proceed with Juhani as though she were any other party member.
I really should look at that dialog more closely.... it can't be that hard to fix well, and though I know it has been done a couple times, it has never been done to my full satisfaction.... hmm...