Hard to answer without reading the manuscript, but I agree that the MC has to grow/evolve somehow. By "one-note," she may have meant that the story is too narrow and doesn't have that lasting impact. Does it linger with the reader enough or convey the "universal from the local," as David Almond once said at a NYC conference? It might be great for a magazine, but if you want it as a picture book that people will buy and reread, it might need more tweaking. Sounds like you're definitely close with it, though, so it might not even need a full overhaul.
I think you could go ahead and send her the other submission ready piece along with a brief thank you. But because she is normally closed, you want to maximize your chances. Before you send that puppy out, have a critique partner review it and make sure it's the best it can be. Good luck!