Leonard did nothing wrong. And, to a degree, so did Manah.
As someone who just played through all the Drakengard games to try and understand them and Nier I can easily say he is the playable character least at fault. He's still not without sin or major faults. You can't sit there and tell me jerking off to the idea of touching kids while having being along with a bunch of little siblings isn't fucked up. Manah, is still responsible for most of the plot happening. What makes Drakengard (and the entire franchise of this and Nier) so great is how even if you can sympathsize with why these people are the way they are. No one is truly a good person. Not even Furiae is absolved from this.
That said it's strange to think that such a cult phenomenon started out so strangely and could have easily been a one and done type of deal if it wasn't for that Madman Yoko Taro...