A president has always had the "military coup" option. In fact, Putin also has the "violent overthrow of the US government" option (though he would probably use his own military).
That said, as I mentioned in a different reply, I should have stuck to the legal implications around impeachment, rather than the practical. This decision states that the only remedy for a president breaking some laws is impeachment. At the same time, it says the president now has a legal, if not entirely reliable, means to avoid impeachment: Order the military to kill those who would impeach them.
Yes, that was always a theoretically practical option, but now it's also a legal option, and that's bad. A strong nation requires a strong legal system.