I met today with Rabbi Friedlander in Yerushalayim. He is well aware of the forged mezuzah problem and suggests that the only 100% guaranteed way not to be duped is to ensure that you buy directly from sofrim you know and trust. He said there are enough sofrim out there that you can deal with them directly and don't need to risk buying from "unknown sofrim" through sochrim and wholesalers.
However if one has no choice and needs to buy from a socher selling 3rd party items, he suggests that you ask the socher for the number of the sofer's teudah (kaballah). The socher has nothing to worry about because Mishmeres Stam will not give out names of sofrim. However Mishmeres Stam will have a copy of the sofer's writing on file. They will be able to tell you if the item you have matches their sample, thereby confirming the sofer is "real" and your product is legit.
For those strict to buy only items written by sofrim with ksav kabbalah, this system should work well not only to weed out any of the forged mezuzos, but also to confirm that the sofer has kaballah. Just email Rabbi Granenstien the sofer's number and a scan of what you got and he will confirm by email that its all good. You only have to do it once per sofer.
Rabbi Granenstien's email address is email@example.com. He happens to be an extremely nice fellow and always happy to assist.