I've forwarded the issue to the design team in case there is something they can do to update this. More than likely it is working as intended but not being very clear in the reward description. The item is unique and you cannot have 2 of them on your character at once, so it needs to clearly state that before you start the mission and before you turn it in.
I just did this on the Klingon side and got ripped off there too!
To add insult to injury my "Ally" turned out to be the federation cruiser, which promptly opened fire on me. I had to get close enough to get the Depart System message anyway.
I was really looking forwards to this Episode and it has completely sucked the fun out of me with bugs and rip offs.
Next time instead of voice talent you need to hire some QA instead.
Better yet, put it on Tribble first, We seem to find bugs way better than you do.
That's not something to expect. These missions are supposed to be a surprise for everyone which is why they do internal testing. This, along with the fact that its an MMO is why we should expect bugs. Its not like any of the other series episodes didn't have bugs when they were first released.
As for your Ally turning out to be a Fed Cruiser, there is a certain level of humor to that :p