Jolene you are totally right to be angry and upset, it must have been scary.
However, I think there are a few issues which are problems with the crèche and I think you should be careful how you raise them, as presumably your desire is to see this does not happen again, rather than simply tell them how angry you are.
As far as I see it there are three issues here, which, in your shoes I would raise with the church.
No, 1 the room used, or boxes of toys brought out, contained a small object not suitable for the age group.This may not be the fault of those helping, I am sure there is not time to examine the boxes of toys or whatever every time. The room should be clean and free of small objects, and any noticed when the helpers come into the room, to set up, removed. I've been in crèche' (not church) where balloons (un-inflated) were in amongst the toys, I removed them all and reported it. Balloons can be a massive chocking hazards. Sadly, balloons are also very popular with kids!
No 2 those helping in the crèche did not notice your child had something in her mouth. We do not know how long it had been there and it may have only just gone in before you came. Niether they nor you checked to see what it was and they wrongly told you it was food.
You did not notice at first either and so it is fair to say that all of you were not totally on the ball that morning. I think you should have looked in her mouth earlier and not assumed it was what the helpers said it was. I think I would have looked first not asked the helpers.
No 3 They served food to your child without checking with you it was OK to do so, e.g. checking she did not have any allergies. Of course if she had allergies you should ideally tell the helpers but probably only if you expected there to be food, it could go either way. This is not something you mentioned as a problem but I think it is only right for helpers to check. If you did not drop her off at the crèche, if your parter or friend did, do check with them this was not discussed before bringing it up with the church.
Whether the crèche is free or paid for, if it is offered you expect excellent, and at the very least safe, care of your child. I expect the church aims to offer that so they should listen to your concerns and act on them.