Here's the answer:
No, you won't have to worry about Pokemon transferred from Diamond/Pearl to Battle Revolution obeying your orders.
* Battle Revolution is a separate game. It's an online battle game where you use a Wi-Fi connection to battle other players.
* Pokemon transferred to Battle Revolution act as "rental Pokemon". They are not connected to your in-game trainer or save data.
* You will control the rented Pokemon in battle, but they will revert to their default movesets and abilities once the battle is over.
Essentially, you're borrowing Pokemon for a battle, not adding them to your team permanently.