Would this then prevent the arduino board from being able to be programmed via the 'high voltage' method? Granted that would represent a very small population of users, however I've seen at least one shield based high voltage programmer avalible for sale. It allows those that have managed to 'brick' their processor by errors in fuse settings, i.e. change reset pin to be a I/O pin, etc.
If it does, it's easy for new design to add two via around the diode to shunt it easily using a basic wire, or even add an open pad to be shunt with solder.
By the way, some diods seem to anihilate the reset for programming, so choosing the right one matters a bit.