I don't think they'll replace Beckett yet. After Frasier, SG1 went a couple of seasons without a regular Doctor. Whenever the team were wounded they either didn't show the doc, or had a "doctor of the week" extra. I think they'll do the same thing with Atlantis.

Then again, it kinda seemed like they were setting up Dr. Cole to take his place. They've never shown her before IIRC.