I don't know the full context of this, but to be fair to Red Skull he does live in a setting where it would not be too far fetched for the child to have world shaking heroic superpowers with which to obliterate him entirely. This may make him seem cowardly, but in the Marvel universe killing a suspicious child is actually the pragmatic choice for a scheming super villain to make.

Some villains stand out because of how powerful they are.
Some stand out due to their clever schemes.
Some stand out thanks to their theatrics and enviable presence.

Some, though, some stand out because they are evil motherfuckers.