He only gets the Black Materia in Northern Crater. Immediately after this he makes his barrier and starts restraining Holy. He had no chance to go after Cloud.
Sephiroth can control Cloud like a puppet at that point. He could literally force Cloud to impale himself if he chose too. Even at the end, he can control the bodies of your entire party. It takes them at least a minute to break free of his control, and he just stands there.

The creators have even stated that Sephiroth doesn't exert any effort on Cloud. O_o

So yeah, it is unreasonable to bash Kuja for doing something that Sephiroth and most FF villains do. Sephiroth just takes it to a ridiculous level.