Oh, please. Jane is already and is always going to be the "secondary" Thor, the shadow, the female version. Keeping the hammer if she's still going to be a superhero is the least they can do. The hammer is fundamental to her story, in a way that it wouldn't be for Thor. He's still him and he will stay kinda the same with the Ultimate hammer, except for the unworthy storyline, while Jane's plot is all about how the hammer transforms her from a simple woman dying of cancer to a fabulous(my words) superhero.
Is the same reason why Sam keeps the Cap's main shield. Steve has enough, he has nothing to proove(well, the Hydra plot kinda ruins that a bit, but still, he'll come clean soon), he's already THE Captain America. But, Sam could at least go back to Falcon. Jane as not Thor is just Jane.