It won't fall under the exemption for babiels/toddlers but it May fall into the medical exemption.
In your case I would:
Scour the TSA website for information on the exemptions for medicines, (both OTC and prescription) and see if you can find something to include dietary needs ~ print it out. Consider getting a Dr. Note and bring the papers. Bag the Pediasure separately in a ziplock and only what is "reasonably necessary" for the flight and then declare it at the TSA checkpoint and hope for the best. Bring an empty sippy cup and get ice after security or from the FA.
However:
Depending on how long your flight is and if she can get by for a while with juice or water I would not try and bring the pediasure unless it was absolutely necessary.
I don't know how often you fly, I fly monthly at least and IMHO getting through the checkpoint these days is stressful enough, I would work on preparing your dd and knowing the procedures yourself and making things as easy as possible. I hardly even bother with a 3-1-1 bag anymore! I wouldn't complicate the procedure unless it was absolutely necessary. JMHO