I'm not sure how to make it a happier experience for her, but what I can tell you is that I sort of went through the same thing recently with my daughter. She started a parent's day out and this would be the first time she was without me, so I dreaded the first day. Well, it was fine, she couldn't get rid of me fast enough. Then all of the sudden, two months later, she no longer wanted to go to "school". She would tell me over the weekends how she did not want to go back to school the following week. I had to leave her with her teacher screaming and crying...that about killed me. It only happened about 3 or four times and then she stopped being so upset and began to enjoy it again. Not sure what happened exactly though. I started talking to her about it and being very positive about the whole school thing and meeting new friends, etc. I just guessed it to be her shyness. Maybe she wasn't sure how to socialize and make new friends (she's VERY shy) and felt left out, I really don't know. I talked to her teachers and they seemed to think she was doing fine. And then again, perhaps being away from me finally caught up to her.
I'd just keep talking to her about Sunday School, stay positive and pray about it. She'll eventually work through it.
good luck