I'd be less concerned with the weakened rotor as I would to getting the holes perfect and concentric; it's a fairly common practice to re-drill rotors.

If you have a good quality drill press, precision center punches, and a precision alignment jig (just a cylinder to slide into the centers) then I'd say go for it.

Otherwise, send it to a machine shop.

Some folks say brakes are important. But hey, a 20s era board track Indian didn't have any at all.

Pick your comfort level.