I really don't know what to say to that. Everything about about agriculture or gardening or domestication is changing or at least redirecting biological drives to suit our purposes better. That can be done in a cruel way, but I don't think it is an inherently cruel activity. I'm not sure when I would call doing something to a plant cruelty.
A bonsai at least a mature tree that goes through is whole life cycle, just dwarfed by pruning and limited soil.