I think we should wait till Kunal and Nandini have a proper conversation, that will bring alot of clarity. Ever since their affair got revealed, both haven't talked properly. Now when they meet what Kunal says to her, will tell about his exact thought process or state of mind.
Also i think the reason of Kunal guilt is clear. He is guilty for causing the pain to Mouli. I think he has came back to reality and seen how much his actions have destroyed Mouli. So saying sorry for that and asking for apology. Maybe he wants her to heal and not suffer and thinking how he can do anything to help that. Now i know, many will here say he should get lost lol but probably it's human for him to think like that and much better than having no guilt or shame at all.
This is my theory, i could be wrong in thinking that or the writer tomorrow throws another googly at us like she has continued to do so with the characters of Kunal & Nandini. So let's wait and see