Answer in progress. (Shall expand, and add more authoritative links when have time later).
Modern electronic (as opposed to mechanical) fuel-injection systems (that also includes TBI (throttle body) single-point injection) are equipped with throttle position sensor. In the event of overrun (higher RPM, closed throttle) fuel input is cut off, thus making it more efficient than coasting in neutral and using brakes alone (one supposed to brake with gears engaged anyway). Fuel kicks in only when engine speed (RPM) approaches to or below the idle speed to maintain it.
Information about fuel cut-off operation can be found in Bosch technical publication “Gasoline Fuel-Injection System K-Jetronic” (PDF, search for multiple occurrences of “overrun”):
Fuel metering is interrupted during trailing throttle [overrun]. Although this expedient saves fuel on downhill stretches, its primary purpose is to guard the catalytic converter against overheating stemming from poor and incomplete combustion (misfiring)
Cutoff of the fuel supply during overrun operation permits the fuel consumption to be reduced considerably not only when driving downhill but also in town traffic.
Similar data can be found on systems of other manufacturers. Some of them even allow the cut-off parameters to be modified (see adjustment of overrun for SManager software for s300 module for Honda ECUs — good illustration on how this feature works).
As above suggests, power stroke is eliminated, ergo one of the most demanding energy loads on the engine is gone. In all, given proper care and maintenance, consensus is that engine braking does not add any statistically significant friction wear on the motor itself.
To test this hypothesis I did several searches on the subject via academic databases and Google Scholar (both with and without patents), and I have not found a single paper concerned with increased engine wear, but plenty discussing the methods to increase effectiveness of engine braking, as power of modern engines increased dramatically, and drive-train losses are reduced. As this U.S. Patent 5,146,890 (by Volvo) states (p.1 of “Description”):
When driving in hilly terrain, the wheel brakes should be used as little as possible, primarily for safety reasons. The average speed of the vehicle in hilly terrain is therefore greatly influenced by the available engine braking power, which increases the requirement for a more effective engine brake that will also be capable of reducing wear and tear on the wheel brakes and thereby improve running economy.
Higher RPM by themselves do not mean that gearbox is being pushed beyond its design limitations. Few hills at higher RPM due to engine braking (given smooth transitions when switching) would not cause any more wear than, say, hours on end on the motorway pushing over 120 km/h (75 mph). If mountain roads is your primary area of operation then it would qualify as severe use (just like frequent towing), and would require transmission cooler anyway.