I dont like the logic here. We haven't seen her hit something with her fists harder then a nuke. Also, castle bravo wasn't small.
Put another way, Ghidorah's beams are only hitting a small portion of whatever Kaiju they strike. They can one shot a Kaiju who sits unharmed in pyroclastic eruptions and is strong enough to trigger said eruptions with his struggles and can bust up a city without even touching it.
3 simultaneously fired beams on this level, all hitting the same small concentrated spot dont particularly put Godzilla out of a fight. Not like the single beam did to Rodan.