For anyone who somehow expected the twins to not get powers, you were deluding yourselves from the start. The game slowly and steadily turns every friend of MC into a Superhuman. The moment the Twins were foreshadowed to be the next, it was almost certain that it would be the case.
Now for those who somehow think that the Twins work better as anchors to MC's humanity, I'd say that you are completely missing the scope of the game and you ignore how the stakes are raised in every update. Also human or not human, they will need MC to protect them, that's for certain. That fight of Bernhardt vs Eisheth is probably nothing compared to what will come down the line. Expect to see MC fighting battles with orders of magnitude higher intensity. At this scale, Humans and lesser Superhumans are both specks of dust.
Also you probably completely miss how exciting it is that we finally get Strength Eater content. This category of monsters has been teased constantly since 0.95, it involves a literal god, the Great Ocean, with affinity for water (something shared by the Twins) and it's also explained that the power of the Strength Eaters is relative to their enemies and they will also probably inherit the synchronized evolution thing that the Moon Twins got. This sets up Liz&Amber to become very important players down the line.
They really got the absolute best treament possible. I'd say it's even better than becoming Apostlespawns.
As for their current predicament, I really don't think that there is any reason for concern. Nothing is out of the ordinary yet. Everyone dies as part of the infection and Tanos already explained that this particular process is going to be ultra difficult because he has to synchronize their ascensions, which means that he will have to keep them in a mangled state till the time is right to allow them to evolve. So no matter how grim the scene looked, I don't think that there is any reason to believe that something will go wrong.