Hmmm, that is a toughie. The miniatures game is "turn based" so making it an RTS just seems like it is a different game with the same name.
I have yet to play a RTS naval combat game that I enjoyed, because naval battle games in real time are not as much fun as I want them to be. Too much sitting around waiting for something to happen then the action starts and then one of the ships sinks or blows up.
I say make it turn based or if you do go the RTS mode, please implement a system that allows the user to pause the game and relay orders.
Now that is an idea! Pause game to relay orders, I do like that one. Funny how something so obvious would bring the 2 worlds together. Our one concern with doing a straight conversion is that the tabletop game is so good that we want to bring something to the... table! (sorry about the un, I'm so sorry!)