A deleted scene more heavily implies that that is, in fact, what happened.
Dean and Mansley both represent a respective positive and negative viewpoint of how trusting people were in the Fifties, particularly when it came to children:
Dean is a counter-cultural Beatnik who could potentially be a bad influence to Hogarth and when the kid turns up in his scrapyard late at night, he promises not to tell anyone, which would definitely raise eyebrows these days. But Hogarth takes an instant liking to the guy and when it's revealed to Annie that her son sneaks out to play at the scrapyard, she seems unquestioningly okay with it. Their trust is ultimately rewarded when Dean puts Hogath's safety at top priority and becomes his stepfather in the end.
Mansley on the other hand is a professional man who works for the government and even though Hogarth immediately despises the man, Annie has no reason to worry about her son's safety even suggesting that he take the stranger on a tour around town. Her trust is ultimately misplaced when Mansley treats Hogarth with increasing hostility going so far as to lie to General Rogard about the Giant killing a kid to provoke a military strike when he knows damn well that the boy is in the crossfire.
Why does Mansley keep using nicknames for Hogarth instead of his real name while pestering Hogarth? Because he thought the name was too stupid for words and is now refusing to use it.
As mentioned under "Foreshadowing," the Giant grouching about having to play as Atomo, instead deciding to play Superman, when he and Hogarth are playing in the junk yard, sums up the entire ending of the movie: he rejects his assigned role of "a big gun that walks" and becomes the hero that he chooses to be.
The gigantic robotic super weapon had to come from somewhere (which the movie never acknowledges). It's likely that those who sent the Iron Giant to earth are not going to just give up after one failed attempt. This deleted scene shows the Iron Giant's memory of him and an army of others of his kind destroying another planet. The fact that the creators were so willing to sacrifice an army of them also strongly hints that there are plenty more of them, too. Also, the end of the movie explicitly shows us that the robots can survive nuclear blasts. And who's to say that he's still friendly after reassembling himself?
The very last image of the film is him giving a friendly smile to the camera. We're fine.
Nothing about the dream or the machine's armaments suggest anything other than that it was sent to destroy planets regardless of inhabitants and that it would use those weapons if anyone tried to stop it. The kid's really lucky that it suffered the damage that scrambled its programming.
All those threats Mansley made against Hogarth while trying to get him to reveal the Giant's location? Despite Hogarth's protest, he probably could do all of them considering Annie's vulnerable position and single parent status.
And imagine how much easier it would have been to carry out said threats if Hogarth wasn't an only child!
In the battle sequence near the end of the film, the Giant's seen blowing up, shooting holes in and deleting from existance several M41 Light Tanks. In each case the animators are sure to show the crews bailing out before bad things happen. The only problem is that the M41 has a four man crew- we only over see the Tank Commander and Driver escape the doomed vehicles, leaving the gunners and loaders trapped and more than likely horribly killed.