It is a choice. You can choose not to get the companion. You can also choose to play a light side imp. Or 4, as in my case. You're not being "forced" to do anything but complete the storyline, and if there's an aspect of the story that requires cross-faction cooperation, then it certainly wouldnt be the first time that happened in the star wars universe.
The real problem is the case of those with their eight character slots already filled by character from a single faction. They're denied the pet due to its designed implementation, and there's nothing they can do to change that other than delete a character and roll something else. That's fairly messed up.
Additional character slots need to be added at the time the new companion is pushed live in order to avoid such situations.