This might be a bit of a necro, but I just wanted to spill my opinions her.
Alot of people who dont believe in this theory, seem to go on about this being a kids game.... Well its a japanese kids game, and japanese culture differs alot from the culture in the west. What might be interesting here is to to read a direct translation of the original japanese-text.
Also the game does not tell you that you killed someone elses pokemon, so small kids would start crying over killing a fictional creature. But It might simply imply it too add some emotional depth to the story. After all this game is not exclusively made for kids, after all you have to be a certain age to understand what is required to play competetive, its an turn-based RPG after all. With many diffrent strategies and tactics.
While a such plot-element would seem too harsh for a game I played while I was 5 years old. It is as mentioned not told directly. yet at the same time Japanese-game producer are one of the most renowned in the world for their brilliant story-writing and game production. Ive never seen Gary have a Cubone, and he would need a Silph Scope aswell.