"Whatever his powers are--or will be--if we train him properly, it can be used for good."
In this context, it means "for good things," "for good purposes." We can guess this because in the world of superheroes and superpowers, there are often supervillains. In any story about a young person who discovers that they have superpowers, we always wonder which way they will use them.
The word "used" gives us the meaning. Things are used "for" a purpose. A screwdriver is used for fastening screws. In a much broader sense, things can be used for "good" in general.
The other meaning of "for good" is like "forever," but it carries a sense of "finished" or "finality." It's often used to mean "to end something finally and permanently."
"It's just a temporary repair, to fix this for good you need to replace the faucet."
That meaning just doesn't make sense in your context.
I suppose we could invent an example, similar to your dialog where it could have that meaning. Suppose there is a magic pill that increases intelligence. Somebody might take this and ask "Will this make me smart for good, or is it just temporary?"
Here are some other examples of the usage meaning "for good, not bad purposes."
In 1942, scientist Harold Urey wrote that he feared that in forty years, looking back, people would judge that "the evil of atomic energy will have been far greater than its contribution for good."
"You can't be near Alex Goddard and not feel a definite sense of carefully controlled power. But is his power being used for good?" (from a novel)
By the way, the dialogue contains a tiny grammatical error, I think. I thought he said "it" can be used for good. Since "powers" is plural, he should have said "they can be used for good."