The federal government regulates firearms under the commerce clause the same whey they regulate pharmaceuticals under the commerce clause. The difference is they can outright prohibit marijuana and not rifles because the latter prohibition would violate the second amendment.

The commerce clause doesn't override the second amendment (or any other part of the bill of rights), there are only cases where a particular amendment was found not to apply.

What you're looking for is emergency powers, but they're not actually in the constitution. In practice what has happened is that Presidents do whatever thing in an emergency and then get sued over it after, and typically lose, but by then it's years later and whatever temporary measures they ordered in the middle of the emergency are long since discontinued.

It's kind of a kludge, but it also kind of works, because it keeps the emergency measures from extending longer than it takes for the courts to catch up to it, and also gives the victims of rights violations the ability to get compensated after the fact for being done wrong in the midst of a big mess.