I like the new rule, GMW gives new bonuses fairly slowly so I don't think it will be game-breaking. I do agree that perhaps they should be moved up one plus.
+2 Bludgeoning/Piercing/Slashing (level 8 with GMW)
+3 Cold iron/silver (level 12 with GMW)
+4 Adamantine (level 16 with GMW)
+5 Alignment based (level 20 with GMW)
Therefore only the highest level casters(20+) could cast a greater magic weapon that blew through alignment based DR. But at the same time it allows higher level characters to overcome some minor annoyances.