We've actually SEEN this happen a number of times; take the Metrons, the Organians, the First Federation, Trelane, the Talosians, the Prophets, even the Q continuum. Starfleet as a rule tries to be on its best behavior when meeting a new species precisely because you never know when YOU might be the primitives in an encounter, and because they remember from their own history how painful it can be when powerful cultures try to dominate weaker ones. And wouldn't you know it: nine times out of ten the semi-god aliens they encounter have either been openly benevolent or intensely ambivalent; the closest thing we see to malevolence is simply callous disregard for life in favor of, say, scientific curiosity (Naguilem), childish pranks, (Trelane), incredibly childish pranks (Q), or a kind of shallow indifference (the Organians). The only time a powerful "new life form" becomes explicitly malevolent is in the example of Gary Mitchel, who is actually a HUMAN driven mad by the sudden explosion of his powers.Meeting alien life is much the same way. You never know when you're going to be the "caveman" in an encounter. What happens when you meet a metacivilization of comparative supermen? Some will aid you, some will hinder you, and most won't care as long as you don't get in their way. Then what do you do? You make sure you're on good terms with the friendly ones because they're the only ones that can protect you from the not-so-nice ones.
It's a concept I sometimes ponder on my own writings, and Frank/Brian Herbert expanded on: humanity is less likely to be dominated by intelligent machines as it is by evil men using intelligent machines.