Very possible we become a scapegoat for Kris
As of Chapter 5, Susie has seemingly considered the possibility that Kris is opening fountains, but she discards the idea because she knows “Kris wouldn’t do that”. This has generally been interpreted by the fandom as Susie being in denial, but I think she’s being pretty reasonable here. Both Kris fountains have put their parents in incredible danger and Asgore was kidnapped because of it. We don’t have a solid answer for why Kris puts their Dad in the sacrifice shelter and we’re literally the friend inside them.
Now imagine that Susie finds out that there is this separate entity that sometimes possesses Kris and makes them do things they don’t want to do. Suddenly the contradiction is solved. Kris wouldn’t create fountains, but “we” would. Kris wouldn’t help kidnap their own parents, but “we” would. Kris wouldn’t betray her, but “we” would.
Granted, this depends on what order Susie gets what information and if Ralsei decides to not spill the beans, so there’s no guarantee this is how the story will play out. But I think it’s pretty in line with the dramatic irony the story is playing with and it’s an easy opportunity for Kris angst. My mental image is Susie telling the soul they’ll never forgive us for all the stuff Kris actually did. Because obviously Deltarune hasn’t tortured this kid enough.
Also I find the concept of Kris’ going “Why would Chara do that?” mildly amusing.