I worked at my son's preschool throughout those years ( I have a degree so that was right down my alley!).  Now, he is entering kindergarten in the fall.  He has never had a crisis since the first one shortly after his birth.  He has been under very good control.  I, too, am not happy with leaving him at school all day.  I will continue my part-time job at the preschool, but I am only 5 minutes away.  (My next mission is to get a job at the school!)  You don't say how long you have had your daughter, but I would be a bit concerned that she has had 2 crisises since you have had her.  Perhaps you should discuss this with her endo.  That should not be happening.  Even when my son broke his leg and later had a severe case of vommiting(rotavirus or food poisoning), he did not go into crisis.  We treated it with stress doses and he was fine. 

Personally, I would encourage you to stay home with this precious gift.  If she spends the better part of her day with someone else, how can you direct someone else to know what to look for?  Knowing my son's past reactions to medical problems and changes in behavior, I feel comfortable now  when I leave him for whatever period of time.  I know what is out of the ordinary for him.  I feel that I can prepare the caregiver to his needs.   Two years may seem like a long time until she goes to school, but I think you will be happy to have done away with a few extras to have had that time with her.  I don't think you are being overprotective at all.  I think deep down you know that you need to get to know her needs better.  And it sounds like you want it that way.  Don't feel guilty for  wanting to stay home.  The more you get to know her needs, you feel more comfortable in letting her spread her wings.  Don't feel you have to hurry!

P.S. Please don't anyone take my statements about staying home vs. working the wrong way.  I would have stayed home with my children regardless of health problems.  However, I do not make judgements to those who do not do as we did.  It is my opinion, am thankful for my choice, and highly recommend the same.