I have drilled out holes before, to do this kind of thing, but you need to be carefull here.
Sometimes, with a plated hole, they use the hole as a "trace", to make a connection between the bottom and top layers. If they do this, and you drill it out, you have just broken the connection. Of course, it can be fixed, you just have to make sure you reestablish the connection when you install the cap.
But, the much easier route is what you said, use a short piece of wire to connect the cap. The problem with wire is that it introduces inductance, which usually defeats the purpose of the cap. So, you need to keep the wire short, or you may be making things worse.
Randy