My full sympathy to you ): Inevitably, when you come out as an atheist you will probably lose one person close to you-but looks at it this way, if they would not tolerate your atheism they are probably people you would not want to be close to.
It's important to be true to yourself. Family and friends who truly love you will stay with you. If you lose them, then they were not worth having anyway. There are new friends out there too! Wishing you the best.