While I don't support the idea, I can see it working easily, and done without completely overhauling the game.
Lets assume that, in the Turn-Based model, every turn represents exactly one minute of real-time. On the player's turn, he/she assigns an action to each unit or structure, which will be carried out when the player declares him/herself done. In turn, each unit or structure completes as much of said task as it is capable of doing in that alotted time.
Example:
Lets examine this idea with two different ships, a capital ship and a frigate scout (the real stats of which are irrelavent in this example). For the purposes of the example, we will assume that the player has assigned each unit to move from one end of a planet's gravity well to the other; a straight line of an equal distance for each ship. Because it is Turn-Based, rather than having a set speed, each ship is set to only travel a certain distance per turn. Thus, in one turn, the capital ship only moves 60% of the distance, while the lighter, faster frigate was able to get there with enough time to have tea.
Now, that may not have been the simplest way of explaining it, try this: The player controls the game during the pauses in action, and the computer plays out those decisions for a set period before allowing the player to intercede with new actions.
See, it can work. Extrapolate the same idea with the ships to other things in the game... Building things: smaller things take 1 or 2 turns to build and bigger things take 3, 4, or even 5 turns to build.
I think this is easily applied to SINS. All youhave to do is tell the game to pause at a given interval, prevent the player from giving commands until the pause comes along, and teach it how to interpret commands based on that system.
In fact, it would make an easy mod and I would love to try it if anyone wanted to have a go.