The use of Bondo is OK for this, to seal the balsa you can use many different sealer. My preference is epoxy. It's available a boat supplies. You can use a cheaper alternative if polyester resin. It is also available at boat supplies as well as automotive parts. You can use clear varnish available at hardware stores (Home Depot, ect). Remember to seal inside and out, as water will find it's way inside the model.

Good luck, you are braver than me in taking on a boat broken in half.