hey writer-at-heart- it was uncomfortable that’s for sure! I dont think he would have said it if he thought you would hesitate to eat by him, so i dont think he meant to put you on the spot. That being said, i dont think you should have lied. Just one reason would be dealing with an invitation when it came- better to nip that problem in the bud. He may have been caught off guard at your answer but i doubt he’s still offended if he ever was. There are jews on alllll places of the full spectrum and im sure he knows not everyone would trust his level. And definitely no need and you shouldnt go apologize. Dont apologize for your frumkeit! You’re not imposing it on him.
As a thought, realize because the range of jews on college is broad, perhaps his comments/psakei halacha you questioned in the past were for a specific individual he believed needed that heter, and may not be halachically assur but something many are machmir on just etc. Just a thought for dan lkaf zchus, but not a reason to change your stance