Actually, the version I heard was that Shooter ordered Claremont to kill off Phoenix because he didn't like the fact that a woman was now the most powerful character in the Marvel Universe. Given the mess he made of Marvel while he was in charge, I don't find that hard to believe.

But Claremont really is a writer of mixed talent; I loved his X-Men run for the most part, but you're right that he resorted to some really stupid plot devices and characterizations just to get that "dramatic scene" (and not just in the Phoenix saga).