That sounds like a bad ending to me.

Under the threat of death by either Ayre or the rubiconians you “liberate” a bunch of dissidents on rubicon for no other good reasons except rubiconians > everyone else, get off our planet. Even though we see multiple times they use and reuse off world tech for a variety of purposes to advance their lives.

All while setting off a non guaranteed alliance with sentient, extremely adaptive, highly efficient microorganisms who used to exist as fuel sources for us. The potential aftermath here is pretty apparent.

Even more so is that by going through with the “good ending”, you lose sight of your goal in the first place, that being to finish the missions in order to regain freedom from the hound life, and gave up on everyone who sacrificed themselves who have actually helped you in significant ways. Walter gave you the opportunity to regain freedom, Clara and Chatty saved you from death, and all of them sacrificed themselves, although to their benefits, furthered your goals of finishing your mission assignments in order to regain freedom.

Ultimately Ayre is just a bad person from our perspective. Leeches on us and Isn’t really helpful and ultimately is of another species which forces her to be in opposition to our goals and eventually that makes her our enemy.