I would reseal the whole thing. Think of it like this, the water has gotten into the silicone and softened it up along the seal there. Now just because there's only a pinhole leak doesn't mean once that's taken care of the problem is solved. The water has contaminated the silicone and from my own experience that means that the seal is no longer trustworthy. While it may be a pain in the ass I would just bite the bullet and redo the whole thing properly. When I redid mine, I was actually surprised to see in some spots that even though it wasn't leaking there was still water between the glass and the plywood.
