From what I gather from what your saying:
You want to parent the thrusters to the ship, yet have the ship move based on the direction the thrusters are pointing?
Well, you can go about this in a variety of ways.
1. Detach the thrusters from the ship but know where they are in relation to the ship. After moving the thrusters simply reposition the ship in relation to where it was from the thrusters.
2. Create a pivot and rotate it as you rotate a thruster. Reposition the pivot instead of repositioning the thruster. After moving the pivot, simply move the ship to the pivot's position.
3. Rethink your parenting. As in first parent the thrusters to the ship, and the ship to a pivot, rotate the thrusters as needed. Then parent the thrusters to the pivot, the ship to the thrusters, and move the thrusters as needed (thus moving the ship) and just to keep everything simple, parent everything to nothing and move the pivot's position to match the ships. Rinse and repeat.
There are a few other ways to go about doing this, but they are more math driven and might be completely off base if I took what you said wrongly, thus they might be a waste of my time to describe.
By the way, this question:
Can you really parent the ship to two parents?
makes absolutely no sense.
Makes perfect sense. I often parent to 1 object and then parent to another to get more control. in essence I have parented to 2 parents for more control.