Had a cleaning yesterday but my mouth seems awfully sensitive?

Yesterday I went to the dentist to have both a cavity filled and a cleaning. It had been several years since I had either done and the filling didn't seem nearly as painful as the cleaning. The lady took this probe and stuck into far into my gums she had said that she was determining if I was in the early stages of periodontal disease. After hearing quite a few fours I became concerned she just told me that she had people who had worse gums than I. I didn't know anything about periodontal disease, and she told me that if the gum is at depth four they don't generally go in and clean the plaque and such out. She also told me I needed to floss on a regular basis and this will help. Well, I have been brushing my teeth after every meal, and flossing too is this more harmful because my gums hurt real bad when I eat or is this part of the cleaning. In other words will my gums toughen up are they just sore because they are in rough shape from my neglect.