They're both probably upset over their pain and confusion for the medicine. How bad are they "hating" each other?? They might just calm down if you spend time with them both in the room. Cats will mark their space and defend it (even a room) so if they understand each other (which they will bc they're both cats) they'll learn to get over it. OR if you can get at a pet store, and find a product called "feliway" which is a cat hormone scent or something.