Fluttershy: "That was Flutter-assisted homicide!" "I'm going to saw through your bones!" "I healed zuh man who will kill you." "Auf Wiedersehen...Schweinehunds!" "All I can tell you about this next procedure is that it will be... excruciating!" "Would you like a second opinion? You are also ugly!" "You have thirty seconds to live!"
Pinkie Pie: "Fight like big mare!" "Fight me, coward!" "Let us wrestle, little mare!" "Put up fists. "Fight me!" "Come; we fight like mare." "Let us fight; mare versus tiny baby mare."
There is only one way to settle this dispute: They must communicate with their hooves! Only in the fires of one-on-one combat can their true selves be shown! It worked for Domon Kasshu. It worked for Kenshiro. Even Goku's been known to do it every now and then. It shall work for Pinkie Pie and Fluttershy!
It shall be a battle so epic that Discord will be able to free himself due to the ensuing chaos, only to turn himself back into stone to avoid getting caught in between their fight. Or they settle their problems through meaningful dialog followed by pastries at Sugarcube Corner. Either way'd be cool.