From the liner notes of the soundtrack CD issued in 2009:
"In the original film, in the lifeboat at the very end of the picture, the girl, Barbara Carrera, turned out to be really a puma, which had been turned into a human being and was now, with the death of Dr Moreau and the inability to arrest the retrogression, this girl that [Braddock] was in love with was inevitably going to become a huge cat. You saw the fangs beginning to appear and it was a really horrible moment, and one that gave the end of the picture a punch and a power, and so the music ended on a great tragic cry. Well, after they previewed the picture in Santa Barbara, the producers saw fit to ... recut it into some kind of ... happy ending. The music of course ends on a tragic note, ... but they didn't have any money to re-record. So it's a very strange ending now, because the music in no way corresponds to the picture."
There's a photo of Barbara Carrerra in the photos of the film on here, showing her with yellow eyes and fangs, so that confirms at one point that they were going to go with the twist ending.
Also, that ending features in the movie novelization by Joseph Silva that I happened upon, but the novel ends even more darkly, seemingly with puma Maria about to pounce and kill him.
I love to love my Lisa.
What?? Did they write a novel of a movie based on a novel?? Oh this crazy world...
Perhaps they will make a movie from the novel they wrote from the movie based on a novel