Well...this is an interesting question. I personally would have established Chloe similar to her Smallville character and playing the part of Clark's sidekick (Lana still is aware of Supes identity so that part of MOS is still intact) the only change that I would make by bringing her into the comic cast is my fan fic idea of having her become the head of Checkmate. In fact in the fac fic Chloe leaves her "civilian" life and organizes Checkmate to provide assistance and oversight of the metahuman community. When Clark finds out he's not very pleased but he comes to understand her decision is due to her experience helping Clark in the past as Superboy she wants to use it to help the other heroes.
As for the temporary excludance of the Daily Planet staff...it makes sense since the main character that they're there to support isn't there at the moment so story telling wise it dtoesn't make much sense to have them around. Once World of New Krypton concludes and Geoff returns to Action Comics to set up his big Superman story for next summer they'll be back.