Since the gear wheels are homogeneous with respect to the material of construction, and lubrication is common to all parts of the gearbox, there is no reason why engine braking places any different demands on a gearbox that when it is transmitting engine power. Hence there is no extra wear from engine braking.
Given the choice I much prefer to use the drivetrain for its intended purpose than to replace brake components an excessive number of times. My brake wear is light, and the fact that I've never had to replace a drive train component convinces me I'm right.