So I guess there was some hope of doing 'The Three Doctors'? Wonder at which stage of the script process this happened?
There were rumors that there were two scripts -- one with the ninth Doctor, one without.
To be honest, I don't find those rumors particularly credible. For one thing, Moffat's not a particularly fast writer, so the idea that he would spend time writing an unusable script is silly.
No, what I think is more likely is that Eccleston politely took two meetings with Moffat. One where Moffat laid out his ideas for the anniversary special and tried to impress on Eccleston how much he wanted and hoped Eccleston would be a part of it. And one where Eccleston expressed his appreciation for being asked and said he was going to pass.