I'm not too worried.
I weighed the rust that came out of both arms and it totaled 703mg. The cranks themselves weigh 383g. So the percent of the cranks mass that is now missing as a result of rust is approximately 0.703/383 * 100 = 0.18%
I'm not sweating it. I will put a bit of rust converter inside the cranks and let it sit a few days. Then my friend, who is an excellent welder, is going to just touch those holes to fill them in. I will then sand them down so they'll be smoother than a baby's bottom and the powdercoater guy will do his magic.
If someone with knowledge and access to CAD software to run some finite element analysis on these cranks to see if the 3mm hole weakens the crank I think we would all be interested in the answer. I'm not going to be hammering these too hard so I'll take my chances.