Don't really see the fuss about Chrono being "beaten up". Sure, it wasn't his fault, but it a rather common comedic reaction to pervyness in manga and anime. If you start fussing about it, why not complaining about Hayate getting a fist to the face just for a little bit of teasing ? Plus, from Fate point of view, she just saw Chrono assaulting Nanoha. Sure, we know it's that potion's fault, but Fate doesn't. How was she supposed to react ? "Oh, sorry to bother you, go ahead." ?
Fun read, looks like this author like to see Fate as completely ignorant of sexuality. XD