Okay, so I actually played this, and no, you defiinitely do not have to create the "pozzed" future. I was entirely able to beat the game creating a future of brutal oppression where trannies are thrown from buildings (because selecting bad options gives you the currency you need to actually decide things), and people constantly die in horrible ways. If anything, this is probably the better way to play, because picking the "good" options results in population explosion and resource scarcity, while doing it my way resulted in "Resource scarcity in 22 trillion years", probably because people were constantly climbing to a population of a few million people before murdering each other down to a few thousand.
You do, however, want to keep them from going totally extinct, and so you PROBABLY want to reduce the destructiveness of their warring down to the point where they don't actually wipe themselves out doing it, but it's totally acceptable and even preferrable to have 99% of them die. You don't have to, in any way, give them a Utopian society. They can all live in hellish dystopias in a cruel universe where God tortures them forever. Especially since the win condition apparently involves everyone being assimilated by the Borg.
Conclusion: It's not quite as comically grimdark as 40K, but it sure as hell is bleak.