If she experienced her relationship with God as being an endless silence, does this not mean, as some atheists have suggested, that she simply lacked courage to face what she should have realized as the truth, based on her own feelings: that there is in fact no God?

Well, no. One's feelings don't dictate what the truth is; at their most accurate, they may be a reflection of some aspect of it, or they may be totally out of whack, for any number of reasons, including chemical. (John Pinnette, roughly: "I don't drink Tequila anymore, because it makes me think I can ski.")