[Archonsod]

At the basic level though, if the flyer is close enough for a melee attack, it's close enough to be attacked back. Who's to say the flier didn't collide with the trampler (imagine the effect of a crow flying into a charging elephant...) and KO itself, or the trampler simply swatting the flier out of the air and proceeding to jump up and down on them?

You don't really need to model a mechanism to take this kind of thing into account to be honest. A dodge chance for fliers (assuming they're agile enough. Not all natural fliers are necessarily good fliers)would be sufficient.