That is not a guaranteed method of preventing ship theft. Even if he orders his crews to do it in time (Goa'uld ships don't have remote self destructs - they change hands often under the reign of the System Lords and that would just be asking for trouble) the self destruct takes time. With access to the engineering core, it can be thwarted. Proper codes are the easiest way, but when you have a Goa'uld on hand to re-arrange crystals, that will work too.