Yes during the next big event they will team up and fury will be back as well. I also wouldn't be surprised if Thor gets back his thorness during an event, but I think female Thor will be around for another 2 or 3 years.
I think they'll revert back to their legacy status once their movies come out. At least for Captain America and Thor
It Happened with with Bucky as Captain America, right before Captain America: The First Avenger Steve became Cap again in Fear Itself. I think once Captain America: Civil War comes out, Steve will become Captain America again.