1. Since religion is neither the only nor most important issue in this country, determining whether or not someone would be "the ideal choice to lead the country" solely according to whether or not they "uphold the separation of Church and State" is not a good idea. There are many other abilities that a president needs to have.
2. Atheists are not necessarily better at dealing with religion fairly than theists. Sam Harris comes to mind as an atheist who, if president, would do as much harm to the relationship between religion and the state many Christians would. For those who don't know, Sam Harris is a very ... vocal atheist who endorses prejudice and discrimination against Muslims because he irrationality ties all Muslims to groups like al Qaeda. Richard Dawkins behaves similarly.
There are also atheists who are, in my opinion, excessively hostile towards Christianity and Christians. There are also atheists who, again in my opinion, are excessively hostile towards all religions, religious people and theists, in general. I would not want those people in any political position anymore than I want religious people in office who think government should be a theocracy.
In short, no, an atheist - simply because he or she is an atheist - would not be an ideal president. An ideal president has to have many qualities and such a president could certainly be an atheist, but their atheism, in itself, is not enough to make it so.