The problem is Thor can only kiill one head at a time, and they will just keep regenerating.
I can accept Thor beating legendary Godzilla, but all of his energy attacks will just make Ghidorah stronger. So he will have to go melee and the regen will cancel anything he does.
I am also not sure if Ghidorah can actually kill Thor, at least not at his base level. Thor is one tough cookie and will be fairly hard to tag at that size .
I am leaning towards stalemate unless Thor does not figure out that he is amping Ghidorah in which case he could eventually make himto strong to beat.
So stalemate for now.
This is the coolest regeneration scene I have seen in a long while.
Ghidorah is 141,000 tons so he regrew like 15-20,000 tons of flesh in like 15 seconds. Deadpool and Wolverine aint got shit on that.