Not for another generation at least.
I sure hope not. That's the last thing America needs. I'm afraid an atheist president would advocate for getting rid of all Christian symbols from the country, such as the Nativity or the Cross, or the Ten Commandments
1-No President could ever get any type of bans through Congress.
2-Even if he somehow did, they wouldn't survive five minutes in court. Making it illegal to display a Nativity scene, cross or Ten Commandments tablet is so blatantly unconstitutional it's tough to describe all the ways. Also most communities in America would refuse to enforce these laws anyway just like Washington and Colorado (and plenty of other places de facto) have agreed to quit enforcing marijuana laws.
I should probably also note the PM of Australia has never even proposed anything even remotely close to what you described.
and while he wouldn't shut churches down, he would actually discourage going to church.
I don't think anyone who currently goes to church is going to quit because the President says not to (even ignoring just how fierce the blowback would be and the electoral price he would pay for such a thing.)
Also once again, the PM of Australia has never done this.
He would probably take prayer out of the beginning of each Congressional session.
That's not up to the President. That would require a change in the Congressional rules, which Congress would have to pass themselves.
That said, I don't think it will ever happen. I think Christ will be coming back to earth very soon and if He tarries, He won't allow an atheist president.
Why would an atheist President be a bigger deal than all the other atheist world leaders we've had, including some far nastier than any US President could be (see Stalin and Mao for starters)?