Perhaps hackish, but could you have a couple of known vertices inside the center of the engine for which you could detect the actual position (including rotations) at runtime? With two vertices making a line down the center of the engine, you'd have the thruster attack point and the thrust vector. That way you'd have the thruster location/direction slaved directly to the engine pod, so whatever it does, the thruster does too...
Not sure if that's possible in the Orbiter API...maybe not by vertices, but you'd at least be able to do it with a mesh group or two, right?