Out of all the states in India, Kerala does have the most amount of people leaving to fight for ISIS. But India have some of the smallest numbers of people who did so in the first place, the amount of Indian ISIS members is essentially a rounding error compared to the numbers from other countries. While Kerala does have many issues, ISIS recruitment isn't a major one.
In addition, other states in India have a much bigger problem with local Jihaddhist groups and Naxalite militants than Kerala does. All Kerala has to do about wannabe ISIS militants is learn from anti terrorist policies being used to combat other Jihaddhist groups elsewhere in India.