I would have a meeting the Director of the Learning Center and with the main lead teacher also in your child's room. You may want to copy and cc the letter to any other teachers dealing with your child also. This will help get it out in the open and let your concerns be known.
Maybe your child was having a rough time during nap time, however she should have been with the other kids on the floor/on their mats. They should not be making special accomodations for her in the bathroom. The bathroom is inappropriate for a pack and play and not safe. If she needs to be taken out of the room and in time out, someone else needs to help. Sounds like there isn't enough workers to help out and that the teacher is using the pack and play to assist her.
I would think about suggestions on how the teacher/school could better handle this situation. What I would do is present your frustration and concerns in writing and in person. Then, I would see if any changes are made and if it improves over the next couple of weeks, I would see if you can stick it out. I know change is difficult on kids no matter what the situation, so it would be difficult to change locations,teachers,etc.... If no changes are made with your child and how they are dealing with her, then I would look into transferring to somewhere else. If they are uncooperative, I would definitely report them to the State-Department of Protective and Regulatory Services.
Our kids go to a Parent's Day Out program and there is 3 teachers in the kids rooms. We have 2 kids, a 22 month old and a 2 1/2 year old. They go into separate classrooms and each room has 3 teachers. On occasion, when someone is sick, they may have 2 teachers in our Sons room. I know my child doesn't always sleep during nap time. However, he is quiet on his mat and they never move him because he isn't sleeping. One suggestion, I would make is how many teachers are in the room, is there adequate staffing-child/staff ratio? Could your child be moved to another room with another teacher? This may not be an option, our church does the classes by age-your birthdate. We also get a checklist type report on how our child's day went, nap time, lunch-how much they ate, how they played, what they played with,etc... Our church is accredited, which is a higher standard. If you are looking for another preschool, daycare, you might want to look into a place that is accredited and licensed and get some referrals also. I would highly recommend our preschool at our church. If you need more info, let me know. I'll keep you and your situation in our prayers.