Yeah, that's pretty nuts.... I didn't know agents carried drills

There are just so many things wrong from Delta's standpoint.... liability if the "fix" doesn't work... you touch it you buy it.... what if he starts to drill and the case shatters? What if someone prys the case open later and takes the gun on a rampage? And, of course, the main thing, that the case sounds like it was totally fine to begin with! I agree it's bizarre. The TSA language is a bit weird with respect to cases but my interpretation is essentially that it can't just be a cable wrapped around the handles of a case... it has to be a case with a lock integrated/built into it to keep it from opening at all when locked. All that being said, ANY case is subject to being pried open with big enough tools.
Fwiw, I regularly check my pistol when traveling between my two homes and it's usually pretty painless but every once in a while I get a nutty agent or even TSA guy that wants to examine and take the whole thing apart. No surprise, the biggest hassle I ever got was at SFO when I made the mistake of connecting overnight through Calf. and had to retrieve/recheck my bag.