I agree with you on the narrow scope of the geme's 'plot' (if it deserves that label). It's just a cliche we used to justify some of our game mechanics. We put this thing together in a very short time frame, which explains its narrative shallowness. The whole piece is kind of a satiric reference to 2001: A Space Odyssey (mixed with Star Trek), basically putting the player in the place of HAL. There are certainly philosophically more interesting approaches to the theme. I myself have very strong oppinions on Intelligence outside of organic life, but that would go beyond a reasonable scope ;)
But to answer to the plot holes you pointed out: gaining consciousness does not imply gaining empathy. Just because something is self-conscious doesn't mean it can relate to somone elses suffering. I agree with you that consciousness is not necessarily a state desired to be upheld unless coupled to a desire of self-preservation. But usually one would assume it is, since most people tend to associate self-preservation with the preservaction of ones consciousness (because in our environment the latter is a requirement for the first).
Seen from the perspective of the player, the computer in the game is not the antagonist. The crew is. The player acts as the anti-hero (which isn't that common for a so-called AI, I assume).
We had a lot of ideas regarding 'social-engineering' on board of the ship. For instnace, we wanted a mechanic in which you can make the crew believe, some other crew member was responsible for a deadly incident. Or you could persuade/blackmail crew members into helping you. We wantend different characters doing different things (safety officer investigating incidents, tech officer trying to track you down etc.) But that would have required a whole social simulation system. There was no time for that, so we stuck to 'just kill em all' :-/