I'm not sure how I feel about it either. What strikes me is that she was just as human as the rest of us are and the fact that she had doubts and pain is not unlike any of us at a given time in our life. Second thought I have is that being surrounded by so much pain in the people that she was ministering to, it is understandable for her to feel the pain of those people and to question God, much in the same way Job questioned God. She probably prayed faithfully for those people and saw little change, and was hurt by that.
If I has lived her life, I probably would have felt as she did. Imagine being surround by so much pain and people asking your why does God allow this? How do you answer that question to people whose reality is beyond their control before you start to ask God yourself, why do you allow this? However, I think experiencing a crisis of faith is all part of the journey.
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Lamentation 3:24 The Lord is all I have, and so in him I put my hope.