Use the "!" character in the fill comand

We can use the "!" character in many command, such as kill, for exemple

/kill @e[type=!player]

(This command kill every entities, apart the player)

So, my suggestion is to put this for the fill command, for the parameter replace

/fill x1 y1 z1 x2 y2 z2 dirt replace !stone

So with this command, we could make the dirt replace all the blocks except the stone in the given area.