However, I think the flotilla rules are easier to abuse, so using the derelict towing rule would make the game more balanced overall.
I agree. Hooking up a line and getting the towed object behind the towing ship is already easy enough. Towing a heavy object behind a ship should definitely slow the ship down considerably. Speed is already powerful enough in the game, so letting ships with fast base moves tow derelicts at that same speed would just make them even more of an obvious choice when building a fleet. I think applying the derelict towing rules to flotillas would actually make for more interesting fleet builds, as the slower ships would benefit instead.