I strongly suspect that much of the plot was written after the major casting was known (so Moffat could adapt to either Eccleston or Tennant), but I tend to agree that Eccleston likely would have replaced Tennant rather than Hurt's Doctor.
I think Moffat wanted his own Doctor for the role. If it had been McGann or Eccleston, fans of those characters would probably have been upset at the dramatic character revision necessary to make the character work. It had to be someone with a bit of an unpredictability who was "different" from the other Doctors. Plus, an established Doctor isn't a secret (one he will take to his grave).