No, she wasn't an atheist. Truly intelligent people who happen to believe question whether or not there is anything out there believing at all. You can argue though whether or not she had given up that God gives a shit, though, or is personal in nature so that maybe he would've saved some of those poor soles she spent her life helping. I also think if she were an atheist she would have cut practical ties with the church, not partaken in Mass, etc. She'll be a saint before long.