Dear Avira,
How does anybody know what they believe? The Rambam has very strong wording for teshuvah gemura. He doesn’t say by the mitzva of emunah anything like that. So who is to say that I believe more than you, or more than any self proclaimed atheist? Maybe we all are believers, maybe none of us are. This has to be wrong. A mitzvah from HKB”H can’t be so wishy washy.
If someone says they don’t keep mitzvos they don’t lose their chezkas kashrus. So how do we accept that the atheist is an atheist? And if he really is an atheist, and then we can assume that he lies for his own benefit (Because there is no Higher Authority in his mind.) so maybe he is lying and is not an atheist.