I was thinking recently since Ruby and Emerald are additional optional bosses, they are avoidable fights.

That would explain why they don't advance the plot the way Ultima, Diamond, and Sapphire do. But since the other three attack cities, you could understand the cities and party defending themselves.

Emerald and Ruby don't bother people; you have to pick the fights with them. So do they deserve to be killed? Certainly the prizes are nice.