I've actually never heard of many cases where a actor/actresses would be recasted for a role, only to come back later after someone else had just previously played their role.
I'm pretty confident that she'll be in "Thor 2".
In any case, it seems like the film will have its fair share of characters to deal with.
Heck, personally, given that we haven't heard much word about a sequel to Hulk, I would have preferred seeing Betty return and function within SHIELD like how her character did in the Ultimates Cartoon so that we could get some closure to that universe if we don't get a sequel to the Hulk.