For some reason I feel that it will partially happen.
My two concepts as wild as they are is that either Atreus will indeed kill Kratos for some reason but will realise what he has done and find a way to go back in time or reverse the death. Even Perhaps a fight between a good Atreus and an evil/ influenced one that would reset the timeline when he goes back in time
The second is that Kratos takes reincarnation as Jormungandr after death ( yes weird I know)