They will simply make it illegal to alter your gun and you will have to subject your gun for periodic testing just to make sure that you haven't been monkeying with it. No problem, except the back log will mean that your gun will be in the hands of the government for about 5 months a year.
That's only part of it. First off, we have to understand, that, just as you say, this is about much more than a silly idea; and its not about crime or criminals, unless we are referring to the bastards in the Cal DOJ and the Cal legislature who want to put this nonsense into law.
Its about yet another cascade of laws designed SOLELY to hamper or stop the law-abiding citizen from exercising his/her Constitutional rights under the 2nd. Such a cascade, ushered in by any ballistic fingerprint mandate would have to include: only the sale of semi-autos that have the fingerprint technology would be legal; periodic testing (like the damn smog laws) to make sure you have not altered your weapon; felony penalties for alteration; serial numbered gun parts; a total registry of gun owners; making it illegal to conduct private party sales, unless the gun is again tested ; requirement of certified labs to conduct the periodic testing. Probably there are many more that a resourceful legislature could come up with. All of this crap is unconstitutional, but in the land of the 9th Circuit Court, there will be no stopping these miscreants.