Hmm...
Cam't you just, instead of having the attacks use palette 3, make them used one of your four palettes (Applejack/Rarity/Pinkie/Cursor)? For instance, fire uses Applejack, ice (and hot blue fire) uses Rarity, and sparkles (palette swapped ones) uses all four?
I don't know how hard it would be to tell attacks to use certain palettes instead of all using #3, and you should make sure that your pony graphics have palette set up same way as the attacks (for instance, if the attack palettes go light-middle-dark, don't hack the new palette as dark-middle-light) or it will look inverted.