Look at Stephen Hawking and Carl Sagan. These men have pondered interactions with alien species and the conclusions have been that any contact would likely involve aliens treating us no differently than we treat an insect. There’s also question as to whether we could even effectively communicate, since not only our language but our entire way of perceiving things may be incompatible.

So while the “Arena” episode was perhaps simplistic, it’s not unreasonable to assume that an alien species might not only have difficulty communicating effectively, but that their first instinct when confronted by an alien species might be to simply eliminate them. Morality (good and evil) is a human concept and it’s divorced from the reality of evolution. In the world outside the human sphere, morality simply doesn’t exist because there’s no common standard to apply.