I liked that story a lot. It summed up a couple of profound issues: Is it wise to forge alliances with less developed (even aggressive) species? If so - how much are you willing to offer in return for ressources, protection and information? Where is the line of the Prime directive, since any alliance is prone to have an impact on the constellation of power in the sector? When becomes the own survival and the possibility to find a way back home more important than the prime directive? How far can you go to make compromises with half of the crew being not even federation members?
These are great questions. I wonder about the Prime Directive and its validity in their situation often; your question on when it becomes more important for them to get home than follow the Prime Directive specifically. I didn't dislike the episode, I just wish Janeway would have been more vocal when it came to working with Seska. I felt that even if she did cave in and contact her she should have at least vocalized her distrust and apprehension more vehnemently.