Any rules you add into the area just complicate the matter even if they are logical. GW are really going for a simplified look on the rules front, you are right that impact hits (or at least from something like a stegadon) would probably push the entire unit back, and impact hits from a steg would do faaaar more damage than from a chariot, which isn't reflected in the rules. I like the idea of a leadership test, it makes sense, it is still a house rule though. Maybe that leadership test could be simplified to a dice off, still representing the same thing but following the rule of follow the dice if you are unsure.
Although another way to look at it, get something big and heavy. A sword if you have one, or an ax. Charge something and swing at it while charging. Then change the thing you are charging to something imaginary, so you just swing at air. That is what is happening if the unit is burned in the magic phase, the steg is all braced to hit the unit and in full swing, then it isn't there. There is a hell of a follow through, in fact you are likely to hurt yourself or at the very least completely lose balance. This is why I think if you destroy something before the combat phase even starts you won't be overrunning.
Slightly off topic, Empire Total War is good, but the AI is terrible and the balance is a bit off, plus it still has a few glitches in it. Don't rush to buy it, wait for a few more patches and you will be much happier. I mean, at the moment the AI do not know how to land troops from ships, so if you start off as england you don't need to leave ANYTHING at home, woohoo! And watching a 'war' between an AI Francd and England is like watching paint dry except at least with the paint it eventually does something.