The amount of inoperative structural genes is extremely modest compared to the regulatory genes that MAKE them inoperative. Regulatory genes: that's the ticket.
The "Vitamin C" gene and it's mutations in primates has been well studied. If humans and primates required this gene to survive, then evolution would ensure that the gene stayed operative when individuals with mutations died. With an inoperative Vitamin C gene, allowed by a high Vitamin C diet, the gene began accumulating errors, and thus can map species splits and act as a timer.
Arguments about whether the rest of the genome is "junk" or are regulatory genes is irrelevant to studies of this specific DNA sequence.
One thing that IDers ignore is that DNA mutations *do* occur. Without the effects of evolution to correct these errors by allowing individuals with damaging mutations to die, then all "kinds" would have died off from harmful mutations, leaving the earth sterile. This is how evolution "guides" the species DNA along a path of survival, and the corollary is that if the path to survival (i.e. the environment) changes, that the species itself will be guided by the same survival mechanism to change.
Once you demonstrate that the environment via evolution "corrects" the genome to allow survival, and then demonstrate that the environment can vary over location and time, then the fact that evolution of species occurs is obvious.