The OP was talking about trying to take toe clips off pedals.

But even so, drilling the heads off fasteners won't harm anything except the fastener. You do have to be careful not to drill past the head and into whatever it's fastening, but IME drilling metal goes pretty slowly, so it's not difficult. Just wear your safety glasses and put something underneath to catch the metal filings so they don't wind up in your feet later on...

An impact driver would be a good way to go, too. But the first step there is still putting the pedal in a vise. If they're still in the crankarms, it's no wonder she's having trouble.