This is purely me wondering out loud. I have never heard anything one way or the other, but what was Eccleston's relationship with Billie Piper like during their time filming series one? Have either of them ever said anything about it?
*If* they didn't get along, I could see Eccleston maybe not wanting to work with her again. But again, I don't know if they got along or not.
And again, where are people getting this "Moffat treats people like crap" stuff? I've never seen hint of that anywhere, except from some fans making inferences because they don't like Moffat's writing and the fact that he can come off as pretty glib in interviews.