In that example, purpose and result are confused.
Before she had a baby, she left work at 5.00. Then her life changed and she made a decision. 'She left work at 3.00 so that she could take care of her children'. Purpose - no comma.
Then someone comes to her desk at 3.30 and asks 'Where's Nina?' Someone answers 'Didn't you know, she leaves at 3.00, so that she can look after her children.' Result - comma. In your example, purpose and resullt have got mixed up:
leaving early allows her to look after her children (result) but when she was making the decision to leave early, child-care was her purpose. I wouldn't make too much of a Thing of the 'rule' about the comma.