Honestly, when it comes to WHY Contessa left Taylor alive… that's a bit open to speculation. Maybe she felt a bit indebted to the person who did what she couldn't in killing Scion. Maybe she recognized a kindred spirit in someone who sacrificed everything for what they felt was the greater good. Perhaps she thought Taylor deserved at least a somewhat happy life after all she'd been through and given up. And maybe she figured that powerless-Taylor couldn't be a threat, especially after being exported to Earth-aleph.
You know what? If any of those were the case, they should have been hinted at in one of the previous chapters, or maybe, I dunno, Contessa's interlude? This, out-of-the-blue, character-breaking moment lends another layer of impossibility to the ending.
As far as the power removal goes, ordinarily I'd agree with you, except it's Contessa. It's entirely possible for her auto-win power to tell her "This caliber bullet fired at this angle will damage Taylor's brain just enough such that she stays alive, but that the damage and resulting surgery will remove her powers." Sure, ordinarily that'd be ridiculously far-fetched, but Contessa's power makes those 1 in a million chances sure-fire things. The fact is, so long as there might be a way to shoot Taylor without killing her, and there might be a way to remove her powers (which you can't disprove the possibility of)… Contessa can easily make that happen.
Every other time Contessa has used her power, we have been treated to a bit of an idea of how it would have worked. Here? It violates all common sense and continuity. The power is auto-win, but it doesn't let her warp the universe to meet her ends; the power doesn't let her beat up Endbringers and the like, for instance, because there is
no way she could do so, because it is impossible.
As to the latter...again, there was never anything hinting at it, and repeatedly it was shown that you would have to kill Taylor to stop her power, most obviously when Bonesaw's corona-pollentia-disabling dust (which
should have prevented Taylor from controlling her power/bugs
at all) merely made the power clumsier.
Finally, as far as this cheapening Taylor's sacrifice goes… eh. Sure, it's not quite as tragic and memorable as the "Taylor dies" possibility, but it doesn't take away from what she was willing to sacrifice, and regardless, she still sacrificed a ton. Personally, I'm perfectly fine with this ending, and it's nice to see that at the end of the day, after all she's been through, Taylor at least gets to live out her own life.
It does cheapen the sacrifice, but I've argued this point enough with some idiot who thought I was saying that a heroic death was better than an equally heroic life, so I won't expand on it too much.
And while Taylor deserves a happy ending, it doesn't make the story better to fit in a happy ending that does not fit in any way, shape, or form. It goes against the tone of the story, it violates common sense, it pulls tricks out of nowhere just because wildbow wanted to give Taylor an unexpected happy ending.
I'm basing this on the fact that they are designed by Eidolon, who Contessa can not forsee because he has a massive section of Eden's powers, and her power, when unaltered, is equivalent to Scion's instant win power, and, using it, he was able to destroy the Endbringers. Additionally, if Contessa's powers had remained unaltered, she would have been able to know exactly how the formulas would behave because they were also part of Eden.
Contessa's power
is unaltered. It was cast off on accident, before Eden could change any of them. Besides, by your logic, Contessa couldn't defeat any capes made by Cauldron, which means that she should have been defeated by Faultline's crew, which had at least
four Cauldron capes.
Oh, and Scion didn't just have the victory power, an athletic build, and small knives. He also has every other power in existence. Combine instant-win with immense power, and you go well beyond what Contessa could achieve.
Not if Contessa and/or Bonesaw have performed the appropriate surgery during the time that she is dead. I did say kill her and then disable her powers.
And how would they do that? Remember the last time Bonesaw tried to disable Taylor's power?