Speaking as someone totally unqualified (ie. I have no kids), I'd let it go. The food seems pretty healthy and if your little one is not getting jacked up by it then let the kid eat. It's not like she is eating nothing but fruit roll ups, gold fish crackers, and other crap. Also at 3 I am not sure she is ready to understand why food is 'bad' when the other kids eat it just fine. Honestly, I am impressed with your day care provider. She is going way beyond what most care givers would do.
"Corn syrup is everywhere; check your pockets." - Sh*t Paleo People Say
"This really steams my monocle!" - RichMahogany