How is pretending to be an alter to protect your biological sister a bad/negative thing in ANY given context?

To the OP, I dont carry a DID dx, but a close friend of mine does, and I would think that she did a very responsible albeit difficult/awkward thing, had she been in your position.

Sometimes littles need to pretend to be grown ups, so as not be found out. Sometimes one pretends to be the other, because they are with an alter's friend or whichever situation you find yourself in.

Its how you stay safe and survive, and I'm glad your T knows this. (if I have permission to hug)