I always felt that Cloud idolised what Sephiroth had been rather than what he was. Bear in mind that, when he was very young, Cloud wanted to emulate Sephiroth, who at the time was a rational person capable of heroic deeds. In getting to know Sephiroth he experiences what many of us experience when we get to know people we admire - their bad side, their weak characteristics. But that doesn't make that childhood admiration go away and it doesn't stop Cloud wanting to be what Sephiroth had once been. In his mind, he probably still fought a little bit for the time when Sephiroth was a hero, and worthy of worship. Wanting to destroy what Sephiroth has become does not mean he cannot still worship what Sephiroth once was.