I've done that before. I just did it about a month ago on the pair of tenor guitars I posted in the what's on your workbench thread. Not only did I cut into the body, but I gouged the template, too, and had to make a new one. Frustrating to say the least. I try to remind myself that mistakes like these are learning experiences.
Do you have a piece of scrap purpleheart from a cutoff? It looks like the seam in the top is just "above" the damage in your photo. You could route or cut away all of the purpleheart below that seam, down between the pickups, stopping at that really narrow little "bridge" of wood between the pickups. Then, you should be able to glue in a small piece of fresh purpleheart in it's place, and re-route your pickup holes as needed. Since you've basically got a little square "island" of wood that's isolated between that seam and the two pickups, no one should ever know, and the repair won't leave any obvious evidence.
Or just slap on a pickguard!
It looks like you're plunge routing down into the top? For pickups, especially when you're just routing a thin top with an existing cavity in the body core, it makes sense to drill out a majority of the wood, then just use the router to get the shape correct. That way, you can make your first router pass with the bit comfortably low enough to make sure the bearing engages the template, without having to plunge into solid wood, which can be risky.
