Again....it's not about what the character was written to be. You could probably surmise her out to be more essential to the story, on paper, than Paltrow's Potts was to Iron Man. But the latter felt better, they made a cuter and more fun pair, and left something that you really wanted to enjoy watching develop more. I really didn't see Thor having that. Granted, that's a lot to measure up to with those two actors...but even still, Thor's felt pretty obligatory in comparison. Not necessarily terrible, but just there, regardless how important it was supposed to be. On the level of Connelly and Bana in Hulk, even though Thor was a better movie.
That's what makes her replaceable, in that despite the kinds of things you mention...it really wouldn't take much to overcome it with someone else of notable name and appeal. Have the next Thor movie primarily not take place on present Earth. There you go. If no Portman, maybe he and Johannsen's character may start spending a little more extra-mission time together in an otherworldly battle or something.
But she's Natalie Portman...of course they'll want her back...because she's Natalie Portman.