Honestly, the South Indian food served in Pondicherry cannot be tolerated by North Indians for long because they are not used to the spices and the tamarind. But the bright side is, that Pondicherry has some amazing places serving North Indian and continental food.
I don't think food is a major obstacle for a North Indian MBBS student at JIPMER. Here is what the food at Pondicherry looks like.
The above pic shows scrumptious Bread and Chocolate, Auroville. The restaurants in Pondicherry are amazing so food should be your last concern here.
As a North Indian, my friend faced some major language issues, especially at the time of applying for ward leave. Her worst experience was the RHC posting during her internship. She had to interact with people in rural areas who spoke a more complex version of the language.
Overall, North Indians might miss their food and interact with their locals but not regret choosing JIPMER despite that!