Ah, so he protected them from being prosecuted or something?

More or less. Not he alone, but many senior LDP leaders with him at the helm.

The murderer wrote.that.he planned to kill the church leader,.but changed.his mine cause Abe was more famous and would get more attention.

Correct.

I don't think there is evidence that the murderers motivations were political, but I could be wrong.

As I understand, he wanted to draw attention to the Moonies while 'punishing' someone he held responsible for his family's condition.