He didn't. It was largely the NRA scaring gun owners to go out and buy more guns, because that is what helps gun manufactures.
He literally wished he could implement Australia's gun control program - which is a de-facto gun ban - in America, on live TV.
How is that not a threat to the Second Amendment?
You do know implementing laws that ban guns don't actually mean the government is breaking into your home to take away your guns. Whether or not you agree with the proposal is different from the fact that Obama never threatened to take away people's guns.
Plus Obama has said this at the beginning and the end of his presidency.