No. You've got totally legitimate points and in some ways, I agree with you whole heartedly. For instance, growing trees for lumber or using grafting techniques to cultivate fruit. Also, consider weeding or fighting back invasive species. But I think in both those cases, we're manipulating plants for more meaningful reasons than just aesthetics. I'd be comparing apples and oranges at this point, but I'd liken it to raising animals for meat or hunting. If we raise animals in a healthy or humane manner or hunt responsibly, it's different than say factory farming or poaching. With bonsai, I personally feel that manipulating a tree strictly for aesthetics isn't a good reason. It's pruned in such a way, it's roots cut back in such a way, that it is very unnatural and it goes through growth not because of how it's treated, but despite it. It's will to live, to thrive, is so strong yet we're taking that will for granted.
I'm not sure when I would call doing something to a plant cruelty.
Well, comparisons don't always hold up, because its apples and oranges comparison again, but I think some of the considerations we give to animals, we could extend to plants. Such as, we should consider its right to live and grow and thrive, its needs for a healthy environment, etc. I always frame the question as "am I being respectful to the fact that this is a living thing?" Sometimes I don't even know.
Like I said, it's a tree, and I don't hold this viewpoint so strongly that I think people who engage in bonsai are monsters, but I also don't think bonsai gives trees the consideration and respect they deserve.