I'm pretty sure Rogue wouldn't even have appeared in Ms. Marvell and that she was created to be a Ms. Marvel antagonist after Carol was exiled into Limbo. I know Marvel created a couple of Ms. Marvel stories that show Rogue with Mystique and Destiny , but only issue #24 was completed when Ms. Marvel was cancelled -- and the stories showing how Rogue came to ambush Carol were created years after Ms. Marvel was cancelled.
And recall that Dave Cockrum had just designed Carols' new black costume for issue #20. The book was cancelled after issue #23 was published. So very unlikely any more changes were in the works.
So, no. I don't think Claremont had any intention of changing Carol into Binary when he was writing Ms. Marvel. It is surprising this hasn't been covered in an interview with Claremont. Maybe he doesn't do interviews?