That is entirely reasonable, but as I mentioned before, it just doesn't make sense that everything important is still in operation after millions of years. It is simply impossible, given the laws of probabilities. No matter how small a chance you assign to a drive module failure, the vastness of time that has passed means that at least one drive module should have failed before now. I made up some numbers before, a billionth of a percent chance of failure doubling every 100,00 years; I think we can all agree that is eye poppingly robust. Yet after 5 million years, even that small chance has grown to the point where it is impossible that there has not been a single failure (and the Destiny could be as much as 50 million years old).
If they had gated aboard, and been confronted with a situation where they were down to 2 or 3 of the original 16 drive modules, multiple shield generators had failed, you know, actual failures in critical systems, then you can make the case for no self repair. But 100% of critical systems were in operation. There is just no way to make that work without some repairs being done, and the database does say the Ancients were never aboard. Self repair seems more likely than some benevolent alien race setting Destiny right, and just leaving it to continue on its way.