I see your point, I would also not want harm Onbu if I can. But since it is not required to have any of these machines, its totally fine, I've seen tech trees with more worthless stages inbetween. In The Wandering Village I can decide at least if I want to have these things, since it is separated from the rest of the techs.
I would find it interesting to see, if there would be a mechanic, where Onbu is reacting more on these harmful devices. Every big animal is trying to get rid of flys or parasites by waving its tail or scrubbing against walls and trees. Onbu could do the same. The benefits of harming Onbu come then with the disadvantage of losing people or buildings.
