Dan,
The Seadoos can be towed however you will have to close off a cooling tube prior to towing. In a case like yours I would install a simply valve that you can simply close off before towing. You'll want to make darn sure however that you re-open the valve prior to running boat. The owners manual identifys which tube to pinch off prior to towing. See, the pump has a tube that sends water up to the exhaust manifold to cool it. If you have an open exhaust valve and send water into the the manifold without the engine running you could possibly fill a cylinder with water. When towing the boat above a given speed you could put enough pressure in the pump to send water up to the manifold. So again to answer your question....Yes you can tow your boat but be sure to either pinch the tube closed or add a valve of some sort to that hose.
Craig