No, she said she could stop them from being hurt. At the end Kreia refused to le the bond work, she used her last energy to make sure the Exile wouldn't die but she would. To quote Kotor2.com
She is, in fact, quite willing to sacrifice herself if it means the player will survive and reconnect with his teachings.
The first part... She is willing to die for him, always had been. Besides just days earlier she knocks the Exile out in a second but then later on she can't even hurt him with the force? Hightly unlikely.
I dont think the Exile would have snuck in and stabbed Sion in the back. Sion seems to recognize you even if you are in stealth. Also Sion remarks in frustration why the Exile seems to be stronger after the fourth time you beat him. This is proof that the Exile defeated Sion multiple times.
What I mean is that perhaps during the fight he managed to get a lucky hit, Like Luke against Vader in ESB, may be he wasn't really superior to Sion at all. The fight is all gameplay so its kinda hard to say how it really happened.
I admit that the Nihilus battle is filled with variables and whatnot, but lets look at the canonical party at the time.Mandalore- Great fighter, but no offense Mandy, you weren't that useful against Nihilus.
Visas: Ok, its possible to sacrifice her, and that may very well be the case if the canonical exile is actually a sith. However that still does not eliminate the alternate possibility.
EDIT: Even in the dark sided case, the Exile is just as strong as in the lightsided version, except he is more ruthless and thus sacrifices Visas. He would still win in a straight out duel against Nihilus.
The alternate possibility places the Exile as a lightsider. In this case, Visas is not much use in the fight because she is not really reputed as a great Jedi. Therefore, one of the alternate paths renders Nihilus defeated largely due to the Exile.
This is not necessarily true, just because the exile is a Jedi doesn't mean he wouldn't sacrifise people for the greater good, he did so on Malachor V and he was still a Jedi back then. Fact of the matter is we don't know if Visas sacrifised herself or not and we don't know how powerful Nihilus was, he could be weak as hell really.