There are also almost predominantly male characters in the Lord of the Rings books and lacked racial diversity, does that mean Peter Jackson should have made Gandalf a female character and made Samwise a black person? Jon Favreau's argument was BS. He just wanted an excuse to cast Scarlett Johansson for marketing profits and because she happens to be a personal friend of his. Kaa was just a shoehorned plot device with the personality of a blank page anyway and had no effect on the plot.
If you ask me, if there was anyone that should have been female, it should have been Bagheera. He is already female in many translations of the books (and I guess the 1967 Soviet animated version really popularized the concept) and he was very warm, caring and empathetic and had a very honeyed voice and was kind of a "motherly" figure to Mowgli. It certainly would be something else than the self-inflated babysitter we got in the Disney remake.
Also, female pythons are not more popular in India. Or any place for that matter, especially since the sexual dimorphism is hard to spot on pythons (though female snakes are usually slightly longer than males. If I'm not mistaken, male Indian pythons usually grow about 10 ft while females usually are about 12 ft. But Kaa was 30 ft long in the books and was able to hypnotize and was more than 100 years old, so the character isn't exactly grounded to reality). In fact, from what I've heard, males are a pretty popular choice since they tend to be more gentle than females, while females tend to be pretty impatient and aggressive, especially during mating seasons.