Should 2001 Toyota sienna XLE dead battery be replaced or recharged - the manual only gives directions to recharge battery - will there be side effects if replaced instead of recharge?

A battery is only an electrical storage device. If the battery is faulty it will not be able to store electrical energy. On the other hand, if the battery is ok, it could be discharged because the alternator cannot create sufficient energy to keep the battery charged. If you are able to charge the battery the problem is in the alternator or an electrical connection. If you can't charge the battery, go ahead and change it. However, replacing a good battery will only make the vehicle run briefly. If the charging system isn't working a new battery won't solve the problem.