Wider editorial pushed the "O5 return as X-Factor" idea. Just as wider editorial pushed the "Jean must die for what she did as Dark Phoenix" idea. Maddie was Claremont's solution to that, as he intended for Scott and Jean(depowered) to retire and live happily ever after. Having Scott leave Maddie and the baby like that was not really his idea.
I never got the sense that Claremont hated Scott. Scott is a consummate leader in the early run, and holds his own against the Mastermind-influenced X-Men in #175. I think Claremont was just bored by Scott after a while, and was more interested in the newer characters.