I can't specifically say why I have no problem with this aspect of the story, yet. Maybe later it'll come to me. It probably has to do with the nature and point of view of the Organians, and the risks to their way of life, from their powers being prematurely revealed to the galaxy.
Do the Organians really seem like the kind of people who would stand up and bellow loudly at the combatants to get the hell off of their lawn, or else? They value their peace of mind, their serenity, and certainly don't want to have to cease to be themselves, every time some obnoxious disruptive conquering army shows up. Maybe they're trying to set an example.
Of what value or interest would EoM be, if it was about a race of people who just told invading armies to get lost, or else? Their powers would still be extraordinary, but they
would no longer be extraordinary, as people. The ep isn't about how amazing their powers are, but about their radically different outlook.
Also, their seclusion and anonymity and quiet existence goes out the window, the moment they reveal themselves. Involuntarily, they become sources of fascination, terror, jealousy, etc, for the whole galaxy. They really have better things to do than become galactic emperors or power-brokers. They just want to live.
They mean it, when they say that exposure to us is painful to them. So they certainly want to avoid having to BECOME us, even temporarily, in order to intimidate and get rid of us. Partly, the episode's about what's wrong with us
... so it's not just a device for prolonging the story when they don't deal with threats to them in the same way that we
Okay, I'm fairly happy with that reply. I tend to figure these things out as I go...