I have read that it is generally bad practice to use your engine to charge your batteries unless the engine is under load (in gear). Does a high output alternator put enough load on the engine so that it is safe to charge on the mooring/anchor?
Operating a diesel engine with no load or constant low RPM is bad. I believe what happens is called wetting in the cylinders. As to your question of a high output alternator that depends. How high and what size engine you have? Most small engines under 36 horsepower the biggest alternator one can put on without major modifications is 100amps. Over that amperage, one needs to put on a double pulley system or two alternators opposite of each other. One will lose about 3 Horsepower on the engine for high output alternators. 3 horsepower is not a big load on the engine.
Having said all that, charging the batteries using only the engine can be done. One has to remember that max output on a alternator is not achieved until around 80-90% of engine RPM. So running at that RPM is better for the engine than idle or low RPM. Second, I would recommend run your engine under full load (motorsail) for a time afterward to clear out any wetting process that takes place. If most of your hours on the engine is charging the batteries I would find another way to do that i.e.; generator, solar panels.
Diesels are not that delicate! Running one under a light load (like an alternator) is not good for the engine, but not dangerous. Mostly what happens is a buildup of carbon fouling. You can spend a winter in the Bahamas, living on the anchor, using the engine only for charging, and the engine will survive. Lots do that. The next time you spend some time motoring at full power, it will probably clean itself out. But notice the "probably". It is more important to run the diesel at full cruising rpm when you are using it for propulsion.