Even assuming "defect" (never mind how Darwinism accounts for the notion of something not functioning as it "ought" to) it still assumes that the inactivation is the result of a mutation, that the mutation is random (not caused by some mechanistic viral or enzymatic activity) and says absolutely nothing about how the ancestor that possessed the purportedly functioning gene came to exist, whether it descended from a universal common ancestor, descended from one of many independently created organisms, etc.
Just because there may not be a plausible alternative explantion readily apparent at present doesn't mean that one's preferred hypothesis of universal common descent should be considered, for all intents and purposes, proven. That's a logical fallacy. It could still be possibly true (in spite of the logical fallacy) but not because of it. It is simply impossible at present to calculate the probabilities of independent occurrences of inactivating mutations because of lack of complete knowledge of all past and present mechanisms of mutation. (There is evidence of insertion bias in some ERV's for example.) So the conclusion of common ancestry based on this line of evidence should be considered, at best, one tentative alternative.
Cordially,