Although Peppers was dealing with the Celestial Trickster in another separate dimension, the troops that were under Krishna's influence were still going strong. There was nothing that was stopping them from working despite the supposed distance away from their 'controller'.
Even Milk had thought that Peppers made a brilliant move by pushing Krishna into her dimensional instance and possibly breaking the spell away from the mind control influence.
Unfortunately, it did not work so she either had to knock all of them down or... there is actually no other choice. However, she was not alone in this matter, Kalki and Parashurama had stated that they would help bear the consequences of Milk and the rest of Jin's army.
