Simple answer - they didn't want to have to explain what happens when a Pokemon that has mega evolved has it's mega stone knocked off.
If it reverts, why? If it doesn't, why not? When does it change? What about changing stats, does a drop in defence make knock off do more damage or does that happen after damage? Etc etc. It is far simpler for them and for us to make it an exception to the rule when it comes to knock off.
