As Major Anri already gets caught in the Republic Questline, I do think there's a little more to all of this than we know so far.
Gnost Dural is alive and well after Ossus. In the Republic questline it seems like he was simply mortally wounded and then left in the library to die. That isn't very remarkable if you canonically chose to kill him as Imperial, because after stabbing him, you just leave. But if you take him alive, it's Anri that gets the order to take care of him.
After catching and imrisoning Anri on Mek-Sha (as Republican), she escapes, you get a letter that no one knows how this could possibly have happened.
Something is up with Major Anri and I don't think she is what she seems to be at first glance.
On the topic of the OP, I don't completely agree. I do think they went a bit over board with kill options during KotFE/ET, but what they need to do is simply make different companions do the same thing, depending on who you kill or not kill. Or make those added on scenes that you get nowadays, if a companion is an exclusive companion. Examples for that are the end of KotET, where if you killed Senya and Arcann Theron and Lana are in the scenes in their place. Or on Mek-Sha, when you are a Mandalorian and chose to let Torian die (for whatever reason.....^^) you still get the little talk about not needing the Darmanda if you have Shae Vizla with you. So the scene was written and implemented with exchangeable compansions in mind. That is fine with me.