Calling Heloise an atheist denies most of what she wrote. She may have been more classically educated than your average ... anyone in the 12th c. basically, and so her stoicism and innovative ideas about intention and the moral and ethical responsibilities of individuals seems a little forward-thinking. However, if we take her at her word, which is all we have of her, she was concerned with how god would judge her consuming devotion to Abelard, and saw her monastic conversion (the second, 'complete' conversion) as hypocrically incomplete, esp. as she was a spiritual leader of others.

edit: i'd suggest the critical work of Betty Radice, one of the prominent scholars/translators of the Letters, for one of the better perspectives on Heloise out there. You'd find, though, if you delved deep, that there are as many explanations and interpretations of the pairs' behavior as there are scholars. H&A are pretty polarizing.