it doesnt necessarily mean she'll end up dead at the end of Thor 2 or Avengers 2. we could easily end up with the same ending that you mentioned from the comics when Jane became a goddess and had to face a challenge and then decided it wasnt for her. Imagine how horrified Jane would be after all of this resolves, especially if she's killed anyone (especially one of her friends) while "under the influence". This would give her a very valid believable reason for saying no to being Thor's lady, and continuing a normal life on Earth.
The Thanos love interest thing is very left field, I admit, but again I am trying to fill in holes and not add in things that would be extraneous here, so that's why I wondered about it. They did already say "to court death" and Thanos smiling which would seem to point towards Lady Death being involved, but I figured that also could simply point to Thanos liking to kills stuff.
And again, they may be reinventing some things and relationships and making it differnt from the comics. But this part of the idea may not be on the nose, I admit that.
As far as the possession itself, the stuntman may not know or be confusing about when she is possessed, again if that is true. Or if not, it could be it's just lurking and watching in the back of her mind, and not making itself known until much later in the film. It is mentioned that both Kosmos and the Beyonder are curious, and so may sit back and just watch things for a while.
I missed the scepter discussion before, but I dont think that rules out the entity within the cube being able to travel through it to a person. It seems like if they were not intending to use the scepter again, then it should not have been so conspicuously missing at the end of Avengers when Loki and Thor returned to Asgard.
as far as this spirit/power being assoicated with the dark elves, again he may be confusing some issues depending on what he's read or seen.
I think I take it as Joss will be twisting a knife in everyone's guts in Avengers 2, as Joss has been known to do.