Agree with Simon, fill the holes and redrill.

What I did on a body of mine was to locate the bridge, drill holes half way through from top towards bottom using an undersize drill, and drill only one all the way through. Then I used the bridge again to drill undersize holes from bottom half way, so they would hopefully meet up with the holes drilled from the top. That way even if they weren't precisely opposite the top they were at least evenly spaced. Then used larger drills to take it out to size, relying on hole following to deal with any major mismatch of the front and back holes, and only taking it out to full size when I was happy the holes from each side were aligning well. A pillar drill is awfully helpful, but mine didn't have the reach to do more than the outside holes, so the rest had to be done by hand.

Another option that occurs to me, if you don't fancy the ferrule block, would be to inlay a piece of veneer or something into the whole area round the ferrules, and make it into a feature.